diff --git a/Dockerfile b/Dockerfile index 550141d..77140db 100644 --- a/Dockerfile +++ b/Dockerfile @@ -13,6 +13,7 @@ USER root # Set the conda environment names to run dependencies ENV CONDA_BAKTA_NAME='bakta' ENV CONDA_GRAPH_ALIGNER_NAME='graphaligner' +ENV CONDA_BANDAGE_NAME='bandage' ENV CONDA_RGI_NAME='rgi' ENV CONDA_EXE_NAME='micromamba' @@ -29,6 +30,8 @@ RUN apt-get update -y -m && \ rgi=5.2.0 && \ micromamba create -n ${CONDA_GRAPH_ALIGNER_NAME} -c conda-forge -c bioconda -c defaults -y \ graphaligner=1.0.17 && \ + micromamba create -n ${CONDA_BANDAGE_NAME} -c conda-forge -c bioconda -c defaults -y \ + bandage=0.8.1 && \ micromamba create -n ${CONDA_BAKTA_NAME} -c conda-forge -c bioconda -c defaults -y \ bakta=1.8.1 && \ micromamba create -n sarand -c conda-forge -c bioconda -c defaults -y \ diff --git a/README.md b/README.md index e99fafd..5af4610 100644 --- a/README.md +++ b/README.md @@ -17,12 +17,12 @@ Sarand can be run using a conda environment or in a container (Docker or Singula - [Bakta](https://github.com/oschwengers/bakta) - [RGI](https://github.com/arpcard/rgi) - [BLAST+](https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download) -- [GraphAligner](https://github.com/maickrau/GraphAligner) +- [Bandage](https://github.com/rrwick/Bandage) or [GraphAligner](https://github.com/maickrau/GraphAligner) ### 1a. Docker This is the easiest way to run Sarand, note that the `-v` argument maps a host directory to the Docker container. -You need to replace `/host/path` and `/container/path` in the command below with the path to the directory containing your input GFA. +You need to replace `/host/path` and `/container/path` in the command below with the path to the directory containing your input GFA. Note that this will also be the location that the output is written to. The most simple way to approach this is by mapping `/host/path` and `/container/path` to the same directory to keep paths consistent. @@ -53,12 +53,16 @@ conda create -n sarand-1.0.1 -c conda-forge -c bioconda -y blast=2.14.0 dna_feat # 2. Create the bakta environment conda create -n bakta-1.8.1 -c conda-forge -c bioconda -y bakta=1.8.1 -# 3. Create the GraphAligner environment +# 3.a. Create the Bandage environment +conda create -n bandage-0.8.1 -c conda-forge -c bioconda -c defaults -y bandage=0.8.1 + +# 3.b. Create the GraphAligner environment conda create -n graphaligner-1.0.17b -c conda-forge -c bioconda -y graphaligner=1.0.17b # 4. Create the RGI environment conda create -n rgi-5.2.0 -c conda-forge -c bioconda -c defaults -y rgi=5.2.0 ``` +Please note that step 3.b is not required if you run the default version of Sarand. Sarand, by default, utilizes Bandage for sequence alignment in the assembly graphs. However, If you prefer to use GraphAligner, please make sure to run command 3.b and install it. **Downloading and updating the Bakta database:** @@ -77,17 +81,19 @@ conda run -n bakta-1.8.1 amrfinder_update --force_update --database /db/bakta/db **Configuring conda environments:** -Here you will specify environment variables that are specific to the `sarand-1.0.1` environment, +Here you will specify environment variables that are specific to the `sarand-1.0.1` environment, these will be automatically used when the environment is active. ```shell conda activate sarand-1.0.1 conda env config vars set CONDA_BAKTA_NAME=bakta-1.8.1 -conda env config vars set CONDA_GRAPH_ALIGNER_NAME=graphaligner-1.0.17b +conda env config vars set CONDA_BANDAGE_NAME=bandage-0.8.1 conda env config vars set CONDA_RGI_NAME=rgi-5.2.0 conda env config vars set BAKTA_DB=/db/bakta/db-light +# Note1: Only run the following command if you have created graphaligner-1.0.17b conda environemnt in step 3.b above. +conda env config vars set CONDA_GRAPH_ALIGNER_NAME=graphaligner-1.0.17b -# Note: Here you can specify an alternate exe (e.g. micromamba, mamba). +# Note2: Here you can specify an alternate exe (e.g. micromamba, mamba). conda env config vars set CONDA_EXE_NAME=conda ``` @@ -100,7 +106,7 @@ python -m pip install sarand==1.0.1 ## 2. Testing -You can test your install has worked by running the test script via `bash test/test.sh` +You can test your install has worked by running the test script via `bash test/test.sh` This will execute sarand on a test dataset (using the following command) and check all the expected outputs are created correctly. `sarand -i test/spade_output/assembly_graph_with_scaffolds.gfa -o test/test_output -a metaspades -k 55` @@ -121,7 +127,8 @@ usage: sarand [-h] [-v] -i INPUT_GFA -a ASSEMBLER -k MAX_KMER_SIZE [-j NUM_CORES] [-c COVERAGE_DIFFERENCE] [-t TARGET_GENES] [-x MIN_TARGET_IDENTITY] [-l NEIGHBOURHOOD_LENGTH] [-o OUTPUT_DIR] [-f] - [--no_rgi | --rgi_include_loose] + [--verbose] [--no_rgi | --rgi_include_loose] [--use_ga] + [--ga] [--keep_intermediate_files] [--debug] Identify and extract the local neighbourhood of target genes (such as AMR) from a GFA formatted assembly graph @@ -130,35 +137,50 @@ optional arguments: -h, --help show this help message and exit -v, --version show program's version number and exit -i INPUT_GFA, --input_gfa INPUT_GFA - Path to assembly graph (in GFA format) that you wish - to analyse - -a ASSEMBLER, --assembler ASSEMBLER - Assembler used to generate input GFA (required to correctly parse coverage information). It can be one of the following options: metaspades, bcalm and megahit + Path to assembly graph (in GFA format) that you wish + to analyse + -a {metaspades,bcalm,megahit}, --assembler {metaspades,bcalm,megahit} + Assembler used to generate input GFA (required to + correctly parse coverage information) -k MAX_KMER_SIZE, --max_kmer_size MAX_KMER_SIZE - The (maximum) k-mer sized used by assembler to generate input GFA + Maximum k-mer sized used by assembler to generate + input GFA + --extraction_timeout EXTRACTION_TIMEOUT + Maximum time to extract neighbourhood, -1 indicates no + limit -j NUM_CORES, --num_cores NUM_CORES - Number of cores to use + Number of cores to use -c COVERAGE_DIFFERENCE, --coverage_difference COVERAGE_DIFFERENCE - Maximum coverage difference to include when filtering - graph neighbourhood. Use -1 to indicate no coverage - threshold (although this will likely lead to false - positive neighbourhoods). + Maximum coverage difference to include when filtering + graph neighbourhood. Use -1 to indicate no coverage + threshold (although this will likely lead to false + positive neighbourhoods). -t TARGET_GENES, --target_genes TARGET_GENES - Target genes to search for in the assembly graph - (fasta formatted). Default is the pre-installed CARD - database + Target genes to search for in the assembly graph + (fasta formatted). Default is the pre-installed CARD database -x MIN_TARGET_IDENTITY, --min_target_identity MIN_TARGET_IDENTITY - Minimum identity/coverage to identify presence of - target gene in assembly graph + Minimum identity/coverage to identify presence of + target gene in assembly graph -l NEIGHBOURHOOD_LENGTH, --neighbourhood_length NEIGHBOURHOOD_LENGTH - Size of gene neighbourhood (in terms of nucleotides) to extract from the - assembly graph + Size of gene neighbourhood to extract from the + assembly graph -o OUTPUT_DIR, --output_dir OUTPUT_DIR - Output folder for current run of sarand - -f, --force Force overwrite any previous files/output directories - --no_rgi Disable RGI based annotation of graph neighbourhoods - --rgi_include_loose Include loose criteria hits if using RGI to annotate graph neighbourhoods - --extraction_timeout Maximum time to extract neighbourhood sequences of a given gene with default value being -1 indicating no limit + Output folder for current run of sarand + -f, --force Force overwrite any previous files/output + directories + --verbose Provide verbose debugging output when logging, + and keep intermediate files + --no_rgi Disable RGI based annotation of graph neighbourhoods + --rgi_include_loose Include loose criteria hits if using RGI to annotate + graph neighbourhoods + --use_ga Enable GraphAligner (instead of Bandage) for + sequence alignment in the graph + --ga [GA ...] Additional arguments to supply to graph aligner in the + form of --ga key value, e.g. --ga E-cutoff 0.1; + it should be used only if use_ga is set to True + --keep_intermediate_files + Do not delete intermediate files. + --debug Creates additional files for debugging purposes. ``` ### 3a. Output @@ -179,5 +201,5 @@ For each extracted sequence, the first line denotes the corresponding path, wher * `annotation_detail_{AMR_NAME}.csv`: the list of annotations of all extracted sequences for an AMR gene * `trimmed_annotation_info_{AMR_NAME}.csv`: the list of unique annotations of all extracted sequences for an AMR gene * `coverage_annotation_{COVERAGE_DIFFERENCE}_{AMR_NAME}.csv`: the list of the annotations in which the gene coverage difference from the AMR gene coverage is less than GENE_COVERAGE_DIFFERENCE value. - * `prokka_dir_extracted{NUM}_{DATE}`: it contains the output of prokka for annotation of a sequence extracted from the neighborhood of the target AMR gene in the assembly graph. + * `bakta_dir_extracted{NUM}_{DATE}`: it contains the output of prokka for annotation of a sequence extracted from the neighborhood of the target AMR gene in the assembly graph. * `rgi_dir`: contains RGI annotation details for all extracted neighborhood sequences of the target AMR gene. diff --git a/sarand/__main__.py b/sarand/__main__.py index 3da918b..49bb57a 100644 --- a/sarand/__main__.py +++ b/sarand/__main__.py @@ -131,14 +131,20 @@ def main(): help="Include loose criteria hits if using RGI to annotate" " graph neighbourhoods", ) - + parser.add_argument( + '--use_ga', + default = False, + action='store_true', + help="Enable GraphAligner (instead of Bandage) for sequence alignment in the graph", + ) # GraphAligner options parser.add_argument( '--ga', default=None, action='append', nargs='*', - help='Additional arguments to supply to graph aligner in the form of --ga key value, e.g. --ga E-cutoff 0.1' + help='Additional arguments to supply to graph aligner in the form of --ga key value,' + 'e.g. --ga E-cutoff 0.1; it should be used only if use_ga is set to True' ) parser.add_argument( "--keep_intermediate_files", @@ -186,7 +192,8 @@ def main(): log = get_logger() # check dependencies work - assert_dependencies_exist(rgi=not args.no_rgi) + assert_dependencies_exist(graph_aligner = args.use_ga, + bandage = not args.use_ga, rgi=not args.no_rgi) # convert argparse to config dictionary args.run_time = run_time diff --git a/sarand/config.py b/sarand/config.py index 525be8e..17d03ee 100644 --- a/sarand/config.py +++ b/sarand/config.py @@ -10,6 +10,7 @@ CONDA_BAKTA_NAME: Optional[str] = os.environ.get('CONDA_BAKTA_NAME') CONDA_RGI_NAME: Optional[str] = os.environ.get('CONDA_RGI_NAME') CONDA_GRAPH_ALIGNER_NAME: Optional[str] = os.environ.get('CONDA_GRAPH_ALIGNER_NAME') +CONDA_BANDAGE_NAME: Optional[str] = os.environ.get('CONDA_BANDAGE_NAME') CONDA_BLAST_NAME: Optional[str] = os.environ.get('CONDA_BLAST_NAME') CONDA_EXE_NAME: Optional[str] = os.environ.get('CONDA_EXE_NAME', 'conda') CONDA_BAKTA_DB: Optional[str] = os.environ.get('BAKTA_DB') diff --git a/sarand/external/bandage.py b/sarand/external/bandage.py new file mode 100644 index 0000000..4043bb2 --- /dev/null +++ b/sarand/external/bandage.py @@ -0,0 +1,460 @@ +import re +import subprocess +import tempfile +from pathlib import Path +from typing import Optional, List, Union, Dict + +from sarand.config import PROGRAM_VERSION_NA, CONDA_BANDAGE_NAME, CONDA_EXE_NAME +from sarand.util.logger import LOG + +##??????? +_RE_VERSION = re.compile(r'(\d+\.\d+\.\d+[-\w]*)') +#???????? +_RE_RECORD_CLIP = re.compile(r'(.*)_(\d+)_(\d+)_(\d+)$') + + +class BandageParams: + """Parameters for the Bandage software.""" + + __slots__ = ( + 'graph', 'reads', 'outputfile','pathnodes', + 'minpatcov', 'minhitcov','minmeanid', 'maxevprod', + 'minpatlen', 'maxpatlen','minlendis', 'maxlendis', + #'threads', + 'verbose' + ) + + def __init__( + self, + graph: Optional[Path] = None, + reads: Optional[Path] = None, + outputfile: Optional[Path] = None, + + pathnodes: Optional[int] = None, + minpatcov: Optional[float] = None, + minmeanid: Optional[float] = None, + minhitcov: Optional[float] = None, + + #threads: Optional[int] = None, + verbose: Optional[bool] = None, + # maxevprod was noted from sci type in + # https://manpages.ubuntu.com/manpages/impish/man1/Bandage.1.html + maxevprod: Optional[float] = None, + minpatlen: Optional[float] = None, + maxpatlen: Optional[float] = None, + minlendis: Optional[int] = None, + maxlendis: Optional[int] = None, + ): + """ + Args: + graph: input graph (.gfa) + reads: input reads (fasta or fastq, uncompressed or gzipped) + outputfile: arg output alignment file (.tsv) + + pathnodes: The number of allowed nodes in a BLAST query path (1 to 50, default: 6) + minpatcov: Minimum fraction of a BLAST query which must be covered by a query path (0.3 to 1, default: 0.9) + minmeanid: Minimum mean identity of BLAST hits in a query path (0 to 1, default: 0.5) + minhitcov: Minimum fraction of a BLAST query which must be covered by BLAST hits in a query path (0.3 to 1, default: 0.9) + + threads: number of threads to use + verbose: print progress messages + maxevprod: Maximum e-value product for all BLAST hits + in a query path (1e-999 to 9.9e1, default: 1e-10) + minpatlen: Minimum allowed relative path length as compared + to the query (0 to 10000, default:0.95) + maxpatlen: Maximum allowed relative path length as compared + to the query (0 to 10000, default:1.05) + minlendis: Minimum allowed length discrepancy (in bases) + between a BLAST query and its path in the graph + (-1e+6 to 1e+6, default: off) + maxlendis: Maximum allowed length discrepancy (in bases) + between a BLAST query and its path in the graph + (-1e+6 to 1e+6, default: off) + """ + + # Store the parameters + self.graph = graph + self.reads = reads + self.outputfile = outputfile + self.pathnodes = pathnodes + self.minpatcov = minpatcov + self.minmeanid = minmeanid + self.minhitcov = minhitcov + #self.threads = threads + self.verbose = verbose + self.maxevprod = maxevprod + self.minpatlen = minpatlen + self.maxpatlen = maxpatlen + self.minlendis = minlendis + self.maxlendis = maxlendis + + def as_cmd(self) -> List[str]: + """Return the Bandage command for use in subprocess.""" + cmd = [ + 'Bandage', + 'querypaths', + self.graph.absolute(), + self.reads.absolute(), + ] + if self.outputfile: + cmd += [self.outputfile.absolute()] + if self.pathnodes: + cmd += ['--pathnodes', str(self.pathnodes)] + if self.minpatcov: + cmd += ['--minpatcov', str(self.minpatcov)] + if self.minmeanid: + cmd += ['--minmeanid', str(self.minmeanid)] + if self.minhitcov: + cmd += ['--minhitcov', str(self.minhitcov)] + #if self.threads: + # cmd += ['--threads', str(self.threads)] + if self.verbose: + cmd += ['--verbose'] + if self.maxevprod: + cmd += ['--maxevprod', str(self.maxevprod)] + if self.minpatlen: + cmd += ['--minpatlen', str(self.minpatlen)] + if self.maxpatlen: + cmd += ['--maxpatlen', str(self.maxpatlen)] + if self.minlendis: + cmd += ['--minlendis', str(self.minlendis)] + if self.maxlendis: + cmd += ['--maxlendis', str(self.maxlendis)] + return cmd + + @classmethod + def from_cli_args(cls, ga): + """Additional parameters supplied from the command line arguments.""" + d_params = dict() + if ga is not None: + for item in ga: + if len(item) == 2: + d_params[item[0]] = item[1] + elif len(item) == 1: + d_params[item[0]] = True + out = cls() + out.update_from_dictionary(d_params) + return out + + def update_from_object(self, other: 'BandageParams'): + """ + Merge two bandage paramters together, taking the non-None + values from the other object. + """ + for k in other.__slots__: + v = getattr(other, k) + if v is not None: + LOG.debug(f'Updated BandageParams.{k} to {v}') + setattr(self, k, v) + return + + def update_from_dictionary(self, d): + """Add/override the parameters from those supplied in a dictionary.""" + if 'graph' in d: + self.graph = Path(d['graph']) + if 'reads' in d: + self.reads = Path(d['reads']) + if 'outputfile' in d: + self.outputfile = Path(d['outputfile']) + if 'pathnodes' in d: + self.pathnodes = int(d['pathnodes']) + if 'minpatcov' in d: + self.minpatcov = float(d['minpatcov']) + if 'minmeanid' in d: + self.minmeanid = float(d['minmeanid']) + if 'minhitcov' in d: + self.minhitcov = float(d['minhitcov']) + #if 'threads' in d: + # self.threads = int(d['threads']) + if 'verbose' in d: + self.verbose = True + if 'maxevprod' in d: + self.maxevprod = float(d['maxevprod']) + if 'minpatlen' in d: + self.minpatlen = float(d['minpatlen']) + if 'maxpatlen' in d: + self.maxpatlen = float(d['maxpatlen']) + if 'minlendis' in d: + self.minlendis = int(d['minlendis']) + if 'maxlendis' in d: + self.maxlendis = int(d['maxlendis']) + return + + +class BandageResult: + """ + A single entry in the Bandage tsv file. + """ + __slots__ = ( + 'query', 'path_with_start_end', 'length', + 'query_covered_by_path', 'query_covered_by_hits', + 'mean_hit_identity', 'total_hit_mismatches', 'total_hit_gap_opens', + 'relative_length', 'length_discrepancy', 'e_value_product','sequence' + ) + + def __init__( + self, + query: str, + path_with_start_end: str, + length: int, + # float but adds % + query_covered_by_path: str, + # float but adds % + query_covered_by_hits: str, + # float but adds % + mean_hit_identity: str, + total_hit_mismatches: int, + total_hit_gap_opens: int, + # float but adds % + relative_length: str, + length_discrepancy: int, + e_value_product: float, + sequence: str + ): + self.query: str = query + self.path_with_start_end: str = path_with_start_end + self.length: int = length + # float but adds % + self.query_covered_by_path: str = query_covered_by_path + # float but adds % + self.query_covered_by_hits: str = query_covered_by_hits + # float but adds % + self.mean_hit_identity: str = mean_hit_identity + self.total_hit_mismatches: int = total_hit_mismatches + self.total_hit_gap_opens: int = total_hit_gap_opens + # float but adds % + self.relative_length: str = relative_length + self.length_discrepancy: int = length_discrepancy + self.e_value_product: float = e_value_product + self.sequence: str = sequence + + def __repr__(self): + return self.query + + @property + def identity(self) -> str: + return self.query + #return self.name.split(' ')[0] + @property + def path(self) -> str: + return (re.sub("\((.*?)\)", "", self.path_with_start_end)).strip() + + @property + def path_start(self) -> int: + if self.path_with_start_end.startswith("("): + index = self.path_with_start_end.find(")") + return int(self.path_with_start_end[1 : index]) + return 0 + + @property + def path_end(self) -> int: + if self.path_with_start_end.endswith(")"): + index = self.path_with_start_end.rfind("(") + return int(self.path_with_start_end[index + 1 : -1]) + return 0 + + @property + def path_to_sarand(self): + """ + self.path: tsv files from Bandage displays a list of nodes + with -/+ tail and comma separated : e.g., '(1363) 69-, 2193+ (1786)' + Return: + nodes: list of node numbers -> e.g., [69, 2193] + orientation: list of orientation of nodes -> e.g., [-, +] + """ + # Remove text between () + #purePath = (re.sub("\((.*?)\)", "", self.path_with_start_end)).strip() + if len(self.path) == 0: + raise Exception('??') + nodes = list() + orientation = list() + node_list = self.path.split(",") + for node in node_list: + if "-" in node: + orientation.append("-") + else: + orientation.append("+") + node = re.sub("[+-]", "", node.split()[0]) + nodes.append(node) + return nodes, orientation + + @property + def coverage_pct(self) -> float: + """Calculate the percentage coverage of the alignment.""" + return float(re.sub("[%]", "", self.query_covered_by_path)) + + @property + def identity_pct(self) -> float: + """Calculate the percentage identity of the alignment.""" + return float(re.sub("[%]", "", self.mean_hit_identity)) + + @property + def amr_name(self) -> str: + amr_str = self.identity.split("|")[-1].strip().replace(" ", "_").replace("'", ";") + return BandageResult.restricted_amr_name_from_modified_name(amr_str) + + @staticmethod + def restricted_amr_name_from_modified_name(amr_name): + """Lifted from utils to avoid circular imports + TODO: Refactor utils to avoid calls to Bandage? + """ + amr_name1 = amr_name.replace(";", "SS") + amr_name1 = "".join( + e for e in amr_name1 if e.isalpha() or e.isnumeric() or e == "_" or e == "-" + ) + return amr_name1 + + +class Bandage: + """Wrapper to the Bandage software. + https://github.com/rrwick/Bandage + """ + __slots__ = ('params', 'results', 'stdout', 'stderr') + + def __init__( + self, + params: BandageParams, + results: List[BandageResult], + stdout: Optional[str] = None, + stderr: Optional[str] = None, + ): + self.params: BandageParams = params + self.results: List[BandageResult] = results + self.stdout: Optional[str] = stdout + self.stderr: Optional[str] = stderr + + @classmethod + def run(cls, params: BandageParams) -> 'Bandage': + """Runs Bandage with the given parameters.""" + + # Display the command to be run + cmd = params.as_cmd() + + # If this is being run in the Docker container, then activate the env first + if CONDA_BANDAGE_NAME: + cmd = [CONDA_EXE_NAME, 'run', '-n', CONDA_BANDAGE_NAME] + cmd + LOG.info(' '.join(map(str, cmd))) + + # Run the command + proc = subprocess.Popen(cmd, encoding='utf-8', stdout=subprocess.PIPE, stderr=subprocess.PIPE) + stdout, stderr = proc.communicate() + if proc.returncode != 0: + LOG.error(stdout) + LOG.error(stderr) + raise Exception('Bandage binary not found') + + results = Bandage.read_file(params.outputfile.with_suffix('.tsv')) + return cls(params, results, stdout, stderr) + + @classmethod + def run_for_sarand( + cls, + gfa: Path, + reads: Path, + threshold: float, + ga_extra_args: BandageParams, + out_dir: Optional[Path] = None, + #threads: Optional[int] = 1, + ) -> 'Bandage': + + """Default method to run Bandage for the sarand pipeline.""" + if isinstance(reads, str): + reads = Path(reads) + + if out_dir is not None: + params = BandageParams( + graph=gfa, + reads=reads, + outputfile=out_dir / 'bandage', + minpatcov = ((threshold - 1) / 100.0), + minmeanid = ((threshold - 1) / 100.0), + minhitcov = ((threshold - 1) / 100.0), + #threads=threads, + ) + if ga_extra_args: + params.update_from_object(ga_extra_args) + out = Bandage.run(params) + if out.stdout: + path_stdout = out_dir / 'bandage_stdout.txt' + with path_stdout.open('w') as f: + f.write(out.stdout) + if out.stderr: + path_stderr = out_dir / 'bandage_stderr.txt' + with path_stderr.open('w') as f: + f.write(out.stderr) + return out + + # Run Bandage in a temporary directory + else: + with tempfile.TemporaryDirectory() as tmp_dir: + tmp_dir = Path(tmp_dir) + params = BandageParams( + graph=gfa, + reads=reads, + outputfile=tmp_dir / 'bandage', + minpatcov = ((threshold - 1) / 100.0), + minmeanid = ((threshold - 1) / 100.0), + minhitcov = ((threshold - 1) / 100.0), + #threads=threads, + ) + if ga_extra_args: + params.update_from_object(ga_extra_args) + return Bandage.run(params) + + @staticmethod + def read_file(path: Path) -> List[BandageResult]: + + out = list() + with path.open() as f: + for line in f.readlines()[1:]: + cols = line.strip().split('\t') + query = cols[0] + path_with_start_end = cols[1] + length = int(cols[2]) + query_covered_by_path = cols[3] + query_covered_by_hits = cols[4] + mean_hit_identity = cols[5] + total_hit_mismatches = int(cols[6]) + total_hit_gap_opens = int(cols[7]) + relative_length = cols[8] + length_discrepancy = int(cols[9]) + e_value_product = float(cols[10]) + sequence = cols[11] + + obj = BandageResult( + query, path_with_start_end, length, query_covered_by_path, + query_covered_by_hits, mean_hit_identity, + total_hit_mismatches, total_hit_gap_opens, relative_length, + length_discrepancy, e_value_product, sequence + ) + out.append(obj) + return out + + @staticmethod + def version() -> str: + """Returns the version of Bandage on the path.""" + cmd = ['Bandage', '--version'] + if CONDA_BANDAGE_NAME: + cmd = [CONDA_EXE_NAME, 'run', '-n', CONDA_BANDAGE_NAME] + cmd + LOG.debug(' '.join(map(str, cmd))) + proc = subprocess.Popen( + cmd, + encoding='utf-8', + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + stdout, stderr = proc.communicate() + if proc.returncode != 0: + raise Exception('Bandage binary not found') + match_stdout, match_stderr = None, None + if stdout: + match_stdout = _RE_VERSION.search(stdout) + if stderr: + match_stderr = _RE_VERSION.search(stderr) + for match in (match_stdout, match_stderr): + if match: + ver = str(match.group(1)) + if ver.endswith('-'): + ver = ver[:-1] + return ver + return PROGRAM_VERSION_NA diff --git a/sarand/external/graph_aligner.py b/sarand/external/graph_aligner.py index 38b84cc..8665323 100644 --- a/sarand/external/graph_aligner.py +++ b/sarand/external/graph_aligner.py @@ -474,7 +474,11 @@ def read_file(path: Path) -> List[GraphAlignerResult]: seq_strand = cols[4] seq_path = cols[5] path_length = int(cols[6]) - path_start = int(cols[7]) + """ + SK: start_pos has been incremented by one to compensate for exclusive bounds + so that it matches the output from Bandage. + """ + path_start = int(cols[7]) + 1 path_end = int(cols[8]) n_res_matches = int(cols[9]) aln_block_len = int(cols[10]) diff --git a/sarand/full_pipeline.py b/sarand/full_pipeline.py index 800ef36..7166042 100644 --- a/sarand/full_pipeline.py +++ b/sarand/full_pipeline.py @@ -18,6 +18,8 @@ import csv import os import shutil +import collections +import datetime import sys from functools import partial from multiprocessing.pool import Pool @@ -28,6 +30,7 @@ from sarand.config import AMR_DIR_NAME, AMR_SEQ_DIR, AMR_ALIGN_DIR, AMR_OVERLAP_FILE, SEQ_DIR_NAME, SEQ_NAME_PREFIX, \ ANNOTATION_DIR from sarand.external.graph_aligner import GraphAligner, GraphAlignerParams +from sarand.external.bandage import Bandage, BandageParams from sarand.extract_neighborhood import neighborhood_sequence_extraction from sarand.model.fasta_seq import FastaSeq from sarand.util.file import try_dump_to_disk @@ -729,46 +732,169 @@ def are_there_amrs_in_graph( gfa_file: Path, output_dir: Path, threshold: float, - amr_path: Path, + #amr_path: Path, + amr_object, ga_extra_args: GraphAlignerParams, keep_files: bool, threads: int, - debug: bool + debug: bool, + use_ga: bool ) -> Dict[str, List[Dict[str, Any]]]: """ To call bandage+blast and check if the amr sequence can be found in the assembly graph Parameters: - amr_file: the address of the query file - amr_name: the name of the AMR sequence gfa_file: the address of the assembly graph output_dir: the address of the output directory + amr_path: the address of the file containing the sequence of all AMRs from CARD threshold: the threshold for coverage and identity + ga_extra_args: Additional arguments to be supplied to GraphAligner. + keep_files: True if intermediate files should be kept, False otherwise. + debug: True if additional debug files should be created, False otherwise. + use_ga: if true Bandage will be replaced by GraphAligner Return: a boolean value which is True if amr_file was found in gfa_file and the list of paths returned by bandage+blast in which the coverage and identiry are greater/equal than/to threshold """ + cat_file, amr_files = amr_object + amr_names = [extract_name_from_file_name(e) for e in amr_files] + LOG.debug( + 'Checking if AMR gene "' + str(amr_names) + '" exists in the assembly graph...' + ) + output_name = os.path.join( + output_dir, + extract_name_from_file_name(cat_file) + + "_align_" + + datetime.datetime.now().strftime("%Y-%m-%d_%H-%M-%S"), + "") # Run GraphAligner - ga_path = output_dir if keep_files else None - ga = GraphAligner.run_for_sarand( - gfa=gfa_file, - reads=amr_path, - threshold=threshold, - ga_extra_args=ga_extra_args, - out_dir=ga_path, - threads=threads - ) + aligner_path = output_name if keep_files else None + if use_ga: + aligner = GraphAligner.run_for_sarand( + gfa=gfa_file, + reads=cat_file, + threshold=threshold, + ga_extra_args=ga_extra_args, + out_dir=aligner_path, + threads=threads + ) + else: + aligner = Bandage.run_for_sarand( + gfa=gfa_file, + reads=cat_file, + threshold=threshold, + ga_extra_args=ga_extra_args, + out_dir=aligner_path + #threads=threads + ) paths_info_list = read_path_info_from_align_file_with_multiple_amrs( output_name=output_dir, - ga=ga.results, + ga=aligner.results, threshold=threshold, debug=debug, ) return paths_info_list +def process_amr_group_and_find( + gfa_file: Path, + align_dir: Path, + output_dir: Path, + amr_threshold: float, + ga_extra_args: GraphAlignerParams, + keep_files: bool, + core_num: int, + debug: bool, + use_ga: bool, + amr_object +): + """ + Read a group of AMRs, write them into a single file and call bandage+blast for it + to identify them in the graph + Parameters: + gfa_file: the file containing the assembly graph + align_dir: the directory for storing alignment info + output_dir: the directory to store the list of AMRs in a single file + amr_threshor: the threshold for identity and coverage used in alignment + ga_extra_args: Additional arguments to be supplied to GraphAligner. + keep_files: True if intermediate files should be kept, False otherwise. + core_num: the number of cores used + debug: True if additional debug files should be created, False otherwise. + use_ga: if true Bandage will be replaced by GraphAligner + amr_object: the list of AMRs and their ids + Return: + the alignment info for AMRs + """ + g_id, amr_group = amr_object + # read info of the group into a single file + cat_file = os.path.join( + output_dir, AMR_DIR_NAME, "amr_group_" + str(g_id) + ".fasta" + ) + file_group = [] + with open(cat_file, "w") as writer: + for amr_info in amr_group: + amr_seq, amr_title = amr_info + writer.write(amr_title) + writer.write(amr_seq) + amr_name1 = amr_name_from_comment(amr_title) + amr_file_name = restricted_amr_name_from_modified_name(amr_name1) + file_group.append(amr_file_name + ".fasta") + + # Run seq alignment tool (Bandage or Graph aligner) + p_find_amr_align = are_there_amrs_in_graph( + gfa_file=gfa_file, + output_dir=Path(align_dir), + threshold=amr_threshold, + amr_object=(cat_file, file_group), + ga_extra_args=ga_extra_args, + keep_files=keep_files, + threads=core_num, + debug=debug, + use_ga=use_ga + ) + if debug: + try_dump_to_disk(p_find_amr_align, Path(align_dir) / 'debug_p_find_amr_align.json') + + # Remove temporary AMR file + if os.path.isfile(cat_file): + os.remove(cat_file) + return p_find_amr_align + +def extract_amr_infos (amr_seq_title_list, amr_group_id, paths_info_group_list): + """ + process the result of parallel processes of bandage + """ + unique_amr_seqs = [] + unique_amr_infos = [] + unique_amr_paths = [] + for i, amr_object in enumerate(amr_seq_title_list): + amr_name = amr_name_from_comment(amr_object[1]) + id = amr_group_id[amr_name] + restricted_amr_name = restricted_amr_name_from_modified_name(amr_name) + if restricted_amr_name in paths_info_group_list[id]: + LOG.debug(amr_name + " was found!") + path_info = paths_info_group_list[id][restricted_amr_name] + overlap, amr_ids = amr_path_overlap( + unique_amr_paths, path_info, len(amr_object[0]) - 1 + ) + if not overlap: + unique_amr_seqs.append(amr_object[0]) + amr_info = {"name": amr_object[1], "overlap_list": []} + unique_amr_infos.append(amr_info) + unique_amr_paths.append(path_info) + else: + if len(amr_ids) > 1: + logging.error("an AMR has overlap with more than one group") + import pdb + pdb.set_trace() + # add this AMR to the right group of AMRs all having overlaps + for id in amr_ids: + if amr_name not in unique_amr_infos[id]["overlap_list"]: + unique_amr_infos[id]["overlap_list"].append(amr_name) + + return unique_amr_seqs, unique_amr_infos, unique_amr_paths def find_all_amr_in_graph( gfa_file: Path, @@ -778,7 +904,8 @@ def find_all_amr_in_graph( core_num: int, ga_extra_args: GraphAlignerParams, keep_files: bool, - debug: bool + debug: bool, + use_ga: bool ): """ To go over a list of AMR sequences (amr_sequences_file) and run bandage+blast @@ -792,38 +919,80 @@ def find_all_amr_in_graph( ga_extra_args: Additional arguments to be supplied to GraphAligner. keep_files: True if intermediate files should be kept, False otherwise. debug: True if additional debug files should be created, False otherwise. + use_ga: if true Bandage will be replaced by GraphAligner """ align_dir = os.path.join(output_dir, AMR_DIR_NAME, AMR_ALIGN_DIR) os.makedirs(align_dir, exist_ok=True) - - """ - AM: This replaces the original implementation of process_amr_group_and_find - as it's more efficient to run GraphAligner using GraphAligner with multiple - threads instead of multiprocessing workers. - """ - d_amr_to_path_list = are_there_amrs_in_graph( - gfa_file=gfa_file, - output_dir=Path(align_dir), - threshold=amr_threshold, - amr_path=amr_sequences_file, - ga_extra_args=ga_extra_args, - keep_files=keep_files, - threads=core_num, - debug=debug + + # """ + # AM: This replaces the original implementation of process_amr_group_and_find + # as it's more efficient to run GraphAligner using GraphAligner with multiple + # threads instead of multiprocessing workers. + # """ + # d_amr_to_path_list = are_there_amrs_in_graph( + # gfa_file=gfa_file, + # output_dir=Path(align_dir), + # threshold=amr_threshold, + # amr_path=amr_sequences_file, + # ga_extra_args=ga_extra_args, + # keep_files=keep_files, + # threads=core_num, + # debug=debug, + # use_ga=use_ga + # ) + # if debug: + # try_dump_to_disk(d_amr_to_path_list, Path(align_dir) / 'debug_d_amr_to_path_list.json') + + # generate the groups and store the group of each amr + group_num = 5 + amr_group_id = collections.defaultdict(list) + amr_file_groups = [[] for i in range(group_num * core_num)] + amr_title = "" + amr_seq_title_list = [] + # Read AMR sequences one by one + amr_counter = 0 + with open(amr_sequences_file) as fp: + for line in fp: + if line.startswith(">"): + amr_title = line + continue + amr_name = amr_name_from_comment(amr_title[:-1]) + amr_seq_title_list.append((line, amr_title)) + id = amr_counter % (group_num * core_num) + amr_file_groups[id].append((line, amr_title)) + amr_group_id[amr_name] = id + amr_counter += 1 + + amr_objects = [(i, e) for i, e in enumerate(amr_file_groups)] + # parallel run Bandage+BLAST + p_find_amr = partial( + process_amr_group_and_find, + gfa_file, + Path(align_dir), + Path(output_dir), + amr_threshold, + ga_extra_args, + keep_files, + core_num, + debug, + use_ga ) - if debug: - try_dump_to_disk(d_amr_to_path_list, Path(align_dir) / 'debug_d_amr_to_path_list.json') + with Pool(core_num) as p: + paths_info_group_list = p.map(p_find_amr, amr_objects) + + # """ + # AM: The original implementation has been moved into the following function. + # This is because the output from GraphAligner is now from a single execution, + # and no longer needs to be concatenated from multiple executions. + # """ + # d_amr_to_seq = extract_amr_sequences(amr_sequences_file) + # unique_amr_seqs, unique_amr_infos, unique_amr_paths = get_unique_amr_info( + # d_amr_to_path_list, + # d_amr_to_seq + # ) + unique_amr_seqs, unique_amr_infos, unique_amr_paths = extract_amr_infos ( + amr_seq_title_list, amr_group_id, paths_info_group_list) - """ - AM: The original implementation has been moved into the following function. - This is because the output from GraphAligner is now from a single execution, - and no longer needs to be concatenated from multiple executions. - """ - d_amr_to_seq = extract_amr_sequences(amr_sequences_file) - unique_amr_seqs, unique_amr_infos, unique_amr_paths = get_unique_amr_info( - d_amr_to_path_list, - d_amr_to_seq - ) if debug: try_dump_to_disk( [ @@ -1085,7 +1254,10 @@ def full_pipeline_main(params): LOG.info("Starting analysis...") # Convert the graph aligner arguments into a consumable dictionary - ga_extra_args = GraphAlignerParams.from_cli_args(params.ga) + if params.use_ga: + ga_extra_args = GraphAlignerParams.from_cli_args(params.ga) + else: + ga_extra_args = GraphAlignerParams() # extract AMR and alignment information LOG.info(f"Finding AMR genes in the assembly graph: {params.input_gfa}") @@ -1097,7 +1269,8 @@ def full_pipeline_main(params): params.num_cores, ga_extra_args, params.keep_intermediate_files, - params.debug + params.debug, + params.use_ga ) if not unique_amr_files: @@ -1148,8 +1321,8 @@ def get_unique_amr_info( """ AM: This needs to be looked at in more detail, the results from this function differ depending on the order that they are iterated over. - - The current implementation follows the original ordering (i.e. the order + + The current implementation follows the original ordering (i.e. the order that the AMRs are read from the user input AMR file). """ unique_amr_seqs = [] diff --git a/sarand/utils.py b/sarand/utils.py index 01e9b09..aa79cf2 100644 --- a/sarand/utils.py +++ b/sarand/utils.py @@ -14,7 +14,7 @@ import sys import tempfile from pathlib import Path -from typing import List, Dict, Any +from typing import List, Dict, Any, Union from Bio import SeqIO @@ -22,6 +22,7 @@ from sarand.external.bakta import Bakta from sarand.external.blastn import Blastn from sarand.external.graph_aligner import GraphAligner, GraphAlignerResult +from sarand.external.bandage import Bandage, BandageResult from sarand.external.rgi import Rgi from sarand.model.fasta_seq import FastaSeq from sarand.util.file import try_dump_to_disk @@ -624,7 +625,7 @@ def read_path_info_from_align_file(align_file, threshold=95): def read_path_info_from_align_file_with_multiple_amrs( output_name: Path, - ga: List[GraphAlignerResult], + ga: Union[List[GraphAlignerResult], List[BandageResult]], threshold=99, debug: bool = False ) -> Dict[str, List[Dict[str, Any]]]: @@ -649,12 +650,8 @@ def read_path_info_from_align_file_with_multiple_amrs( # AM: Removed the cast to integer before comparison if coverage >= threshold and identity >= threshold: nodes, orientation_list = result.path_to_sarand - """ - AM: start_pos has been incremented by one to compensate for exclusive bounds - so that it matches the output from Bandage. However, this may not need to be - used. Perhaps Bandage should have been -1 instead? - """ - start_pos = result.path_start + 1 + #start_pos = result.path_start + 1 + start_pos = result.path_start end_pos = result.path_end path_info = { "nodes": nodes, @@ -667,7 +664,7 @@ def read_path_info_from_align_file_with_multiple_amrs( if debug: try_dump_to_disk( debug_to_write, - output_name / 'debug_graph_aligner_coverage_identity.json' + output_name / 'aligner_tool_coverage_identity.json' ) return paths_info_list @@ -766,7 +763,8 @@ def check_file(path: str) -> Path: ) -def assert_dependencies_exist(bakta=True, blastn=True, graph_aligner=True, rgi=True): +def assert_dependencies_exist(bakta=True, blastn=True, graph_aligner=False, + bandage = True, rgi=True): """Check all dependencies exist and work""" versions = list() missing = list() @@ -780,6 +778,11 @@ def assert_dependencies_exist(bakta=True, blastn=True, graph_aligner=True, rgi=T versions.append(f'Blastn v{blastn_v}') if blastn_v is PROGRAM_VERSION_NA: missing.append('Blastn') + if bandage: + ba_v = Bandage.version() + versions.append(f'Bandage v{ba_v}') + if ba_v is PROGRAM_VERSION_NA: + missing.append('Bandage') if graph_aligner: ga_v = GraphAligner.version() versions.append(f'GraphAligner v{ga_v}') diff --git a/test/expected_output/AMR_info/sequences/AAC6SS-Ie-APH2SSSS-Ia.fasta b/test/expected_output/AMR_info/sequences/AAC6SS-Ie-APH2SSSS-Ia.fasta index e200e2e..df1509f 100644 --- a/test/expected_output/AMR_info/sequences/AAC6SS-Ie-APH2SSSS-Ia.fasta +++ b/test/expected_output/AMR_info/sequences/AAC6SS-Ie-APH2SSSS-Ia.fasta @@ -1,2 +1,2 @@ ->gb|GU565967.1|-|24979-26419|ARO:3002597|AAC(6')-Ie-APH(2'')-Ia [Staphylococcus aureus] +>>gb|GU565967.1|-|24979-26419|ARO:3002597|AAC(6')-Ie-APH(2'')-Ia [Staphylococcus aureus] ATGAATATAGTTGAAAATGAAATATGTATAAGAACTTTAATAGATGATGATTTTCCTTTGATGTTAAAATGGTTAACTGATGAAAGAGTATTAGAATTTTATGGTGGTAGAGATAAAAAATATACATTAGAATCATTAAAAAAACATTATACAGAGCCTTGGGAAGATGAAGTTTTTAGAGTAATTATTGAATATAACAATGTTCCTATTGGATATGGACAAATATATAAAATGTATGATGAGTTATATACTGATTATCATTATCCAAAAACTGATGAGATAGTCTATGGTATGGATCAATTTATAGGAGAGCCAAATTATTGGAGTAAAGGAATTGGTACAAGATATATTAAATTGATTTTTGAATTTTTGAAAAAAGAAAGAAATGCTAATGCAGTTATTTTAGACCCTCATAAAAATAATCCAAGAGCAATAAGGGCATACCAAAAATCTGGTTTTAGAATTATTGAAGATTTGCCAGAACATGAATTACACGAGGGCAAAAAAGAAGATTGTTATTTAATGGAATATAGATATGATGATAATGCCACAAATGTTAAGGCAATGAAATATTTAATTGAGCATTACTTTGATAATTTCAAAGTAGATAGTATTGAAATAATCGGTAGTGGTTATGATAGTGTGGCATATTTAGTTAATAATGAATACATTTTTAAAACAAAATTTAGTACTAATAAGAAAAAAGGTTATGCAAAAGAAAAAGCAATATATAATTTTTTAAATACAAATTTAGAAACTAATGTAAAAATTCCTAATATTGAATATTCGTATATTAGTGATGAATTATCTATACTAGGTTATAAAGAAATTAAAGGAACTTTTTTAACACCAGAAATTTATTCTACTATGTCAGAAGAAGAACAAAATTTGTTAAAACGAGATATTGCCAGTTTTTTAAGACAAATGCACGGTTTAGATTATACAGATATTAGTGAATGTACTATTGATAATAAACAAAATGTATTAGAAGAGTATATATTGTTGCGTGAAACTATTTATAATGATTTAACTGATATAGAAAAAGATTATATAGAAAGTTTTATGGAAAGACTAAATGCAACAACAGTTTTTGAGGGTAAAAAGTGTTTATGCCATAATGATTTTAGTTGTAATCATCTATTGTTAGATGGCAATAATAGATTAACTGGAATAATTGATTTTGGAGATTCTGGAATTATAGATGAATATTGTGATTTTATATACTTACTTGAAGATAGTGAAGAAGAAATAGGAACAAATTTTGGAGAAGATATATTAAGAATGTATGGAAATATAGATATTGAGAAAGCAAAAGAATATCAAGATATAGTTGAAGAATATTATCCTATTGAAACTATTGTTTATGGAATTAAAAATATTAAACAGGAATTTATCGAAAATGGTAGAAAAGAAATTTATAAAAGGACTTATAAAGATTGA diff --git a/test/expected_output/AMR_info/sequences/ANT9-Ia.fasta b/test/expected_output/AMR_info/sequences/ANT9-Ia.fasta index 18f8949..4b6fd0a 100644 --- a/test/expected_output/AMR_info/sequences/ANT9-Ia.fasta +++ b/test/expected_output/AMR_info/sequences/ANT9-Ia.fasta @@ -1,2 +1,2 @@ ->gb|X02588.1|+|330-1113|ARO:3002630|ANT(9)-Ia [Staphylococcus aureus] +>>gb|X02588.1|+|330-1113|ARO:3002630|ANT(9)-Ia [Staphylococcus aureus] ATGAGCAATTTGATTAACGGAAAAATACCAAATCAAGCGATTCAAACATTAAAAATCGTAAAAGATTTATTTGGAAGTTCAATAGTTGGAGTATATCTATTTGGTTCAGCAGTAAATGGTGGTTTACGCATTAACAGCGATGTAGATGTTCTAGTCGTCGTGAATCATAGTTTACCTCAATTAACTCGAAAAAAACTAACAGAAAGACTAATGACTATATCAGGAAAGATTGGAAATACGGATTCTGTTAGACCACTTGAAGTTACGGTTATAAATAGGAGTGAAGTTGTCCCTTGGCAATATCCTCCAAAAAGAGAATTTATATACGGTGAGTGGCTCAGGGGTGAATTTGAGAATGGACAAATTCAGGAACCAAGCTATGATCCTGATTTGGCTATTGTTTTAGCACAAGCAAGAAAGAATAGTATTTCTCTATTTGGTCCTGATTCTTCAAGTATACTTGTCTCCGTACCTTTGACAGATATTCGAAGAGCAATTAAGGATTCTTTGCCAGAACTAATTGAGGGGATAAAAGGTGATGAGCGTAATGTAATTTTAACCCTAGCTCGAATGTGGCAAACAGTGACTACTGGTGAAATTACCTCGAAAGATGTCGCTGCAGAATGGGCTATACCTCTTTTACCTAAAGAGCATGTAACTTTACTGGATATAGCTAGAAAAGGCTATCGGGGAGAGTGTGATGATAAGTGGGAAGGACTATATTCAAAGGTGAAAGCACTCGTTAAGTATATGAAAAATTCTATAGAAACTTCTCTCAATTAG diff --git a/test/expected_output/AMR_info/sequences/ErmA.fasta b/test/expected_output/AMR_info/sequences/ErmA.fasta index d09adef..6d4b21b 100644 --- a/test/expected_output/AMR_info/sequences/ErmA.fasta +++ b/test/expected_output/AMR_info/sequences/ErmA.fasta @@ -1,2 +1,2 @@ ->gb|X03216.1|-|4550-5282|ARO:3000347|ErmA [Staphylococcus aureus] +>>gb|X03216.1|-|4550-5282|ARO:3000347|ErmA [Staphylococcus aureus] ATGAACCAGAAAAACCCTAAAGACACGCAAAATTTTATTACTTCTAAAAAGCATGTAAAAGAAATATTGAATCACACGAATATCAGTAAACAAGACAACGTAATAGAAATCGGATCAGGAAAAGGACATTTTACCAAAGAGCTAGTCAAAATGAGTCGATCAGTTACTGCTATAGAAATTGATGGAGGCTTATGTCAAGTGACTAAAGAAGCGGTAAACCCCTCTGAGAATATAAAAGTGATTCAAACGGATATTCTAAAATTTTCCTTCCCAAAACATATAAACTATAAGATATATGGTAATATTCCTTATAACATCAGTACGGATATTGTCAAAAGAATTACCTTTGAAAGTCAGGCTAAATATAGCTATCTTATCGTTGAGAAGGGATTTGCGAAAAGATTGCAAAATCTGCAACGAGCTTTGGGTTTACTATTAATGGTGGAGATGGATATAAAAATGCTCAAAAAAGTACCACCACTATATTTTCATCCTAAGCCAAGTGTAGACTCTGTATTGATTGTTCTTGAACGACATCAACCATTGATTTCAAAGAAGGACTACAAAAAGTATCGATCTTTTGTTTATAAGTGGGTAAACCGTGAATATCGTGTTCTTTTCACTAAAAACCAATTCCGACAGGCTTTGAAGCATGCAAATGTCACTAATATTAATAAACTATCGAAGGAACAATTTCTTTCTATTTTCAATAGTTACAAATTGTTTCACTAA diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/annotation_detail_AAC6SS-Ie-APH2SSSS-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/annotation_detail_AAC6SS-Ie-APH2SSSS-Ia.csv index 65da242..bcd3c8c 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/annotation_detail_AAC6SS-Ie-APH2SSSS-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/annotation_detail_AAC6SS-Ie-APH2SSSS-Ia.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,N-acetyltransferase domain-containing protein,447,554,1000,,10.88545362392296,, -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia,1440,1001,2440,Perfect,10.88545362392296,APH(2''); AAC(6'),yes +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,N-acetyltransferase domain-containing protein,447,554,1000,,10.88545362392296,, +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia,1440,1001,2440,Perfect,10.88545362392296,APH(2''); AAC(6'),yes diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.embl b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.embl similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.embl rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.embl index b041745..674aeef 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.embl +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.embl @@ -14,7 +14,7 @@ CC DOI: 10.1099/mgen.0.000685 CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 07/05/2023, 15:49:25 +CC Annotation Date :: 08/31/2023, 19:06:17 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.faa b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.faa rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.ffn b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.ffn similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.ffn rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.ffn diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.fna b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.fna similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.fna rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.fna diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.gbff b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.gbff similarity index 98% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.gbff rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.gbff index 1b9654f..7fb711f 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.gbff +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.gbff @@ -1,4 +1,4 @@ -LOCUS contig_1 3440 bp DNA linear UNK 05-JUL-2023 +LOCUS contig_1 3440 bp DNA linear UNK 31-AUG-2023 DEFINITION contig_1, whole genome shotgun sequence. ACCESSION contig_1 VERSION contig_1 @@ -13,7 +13,7 @@ COMMENT Annotated with Bakta URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 07/05/2023, 15:49:25 + Annotation Date :: 08/31/2023, 19:06:17 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.gff3 b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.gff3 similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.gff3 rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.gff3 diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.hypotheticals.faa b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.hypotheticals.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.hypotheticals.faa rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.hypotheticals.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.hypotheticals.tsv b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.hypotheticals.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.hypotheticals.tsv rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.hypotheticals.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.json b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.json similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.json rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.json index 93bfef6..7237532 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.json +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.json @@ -112,8 +112,8 @@ } ], "run": { - "start": "2023-07-05 15:49:14", - "end": "2023-07-05 15:49:25" + "start": "2023-08-31 19:06:07", + "end": "2023-08-31 19:06:17" }, "version": { "bakta": "1.8.1", diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.tsv b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.tsv rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.txt b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.txt similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-49/neighbourhood_extracted1.txt rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-06/neighbourhood_extracted1.txt diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/coverage_annotation_30_AAC6SS-Ie-APH2SSSS-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/coverage_annotation_30_AAC6SS-Ie-APH2SSSS-Ia.csv index a3463c8..3547bbe 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/coverage_annotation_30_AAC6SS-Ie-APH2SSSS-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/coverage_annotation_30_AAC6SS-Ie-APH2SSSS-Ia.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,10.88545362392296,447,554,1000, -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,10.88545362392296,1440,1001,2440,yes +seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,10.88545362392296,447,554,1000, +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,10.88545362392296,1440,1001,2440,yes diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/gene_comparison_30_AAC6SS-Ie-APH2SSSS-Ia.png b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/gene_comparison_30_AAC6SS-Ie-APH2SSSS-Ia.png index 5432d53..1d2413c 100644 Binary files a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/gene_comparison_30_AAC6SS-Ie-APH2SSSS-Ia.png and b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/gene_comparison_30_AAC6SS-Ie-APH2SSSS-Ia.png differ diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.json b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.json similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.json rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.json diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt rename to test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt index 1eb573a..bcf2613 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt @@ -1,2 +1,2 @@ -ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note -FKBKAJ_00010 bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia Perfect 900 969.148 AAC(6')-Ie-APH(2'')-Ia 100.0 3002597 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation APH(2''); AAC(6') MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 100.00 gnl|BL_ORD_ID|1714|hsp_num:0 1814 +ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note +FKBKAJ_00010 bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia Perfect 900 969.148 AAC(6')-Ie-APH(2'')-Ia 100.0 3002597 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation APH(2''); AAC(6') MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD MNIVENEICIRTLIDDDFPLMLKWLTDERVLEFYGGRDKKYTLESLKKHYTEPWEDEVFRVIIEYNNVPIGYGQIYKMYDELYTDYHYPKTDEIVYGMDQFIGEPNYWSKGIGTRYIKLIFEFLKKERNANAVILDPHKNNPRAIRAYQKSGFRIIEDLPEHELHEGKKEDCYLMEYRYDDNATNVKAMKYLIEHYFDNFKVDSIEIIGSGYDSVAYLVNNEYIFKTKFSTNKKKGYAKEKAIYNFLNTNLETNVKIPNIEYSYISDELSILGYKEIKGTFLTPEIYSTMSEEEQNLLKRDIASFLRQMHGLDYTDISECTIDNKQNVLEEYILLRETIYNDLTDIEKDYIESFMERLNATTVFEGKKCLCHNDFSCNHLLLDGNNRLTGIIDFGDSGIIDEYCDFIYLLEDSEEEIGTNFGEDILRMYGNIDIEKAKEYQDIVEEYYPIETIVYGIKNIKQEFIENGRKEIYKRTYKD 100.00 gnl|BL_ORD_ID|1714|hsp_num:0 1814 diff --git a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/trimmed_annotation_info_AAC6SS-Ie-APH2SSSS-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/trimmed_annotation_info_AAC6SS-Ie-APH2SSSS-Ia.csv index 65da242..bcd3c8c 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/trimmed_annotation_info_AAC6SS-Ie-APH2SSSS-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_AAC6SS-Ie-APH2SSSS-Ia_1000/trimmed_annotation_info_AAC6SS-Ie-APH2SSSS-Ia.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,N-acetyltransferase domain-containing protein,447,554,1000,,10.88545362392296,, -extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia,1440,1001,2440,Perfect,10.88545362392296,APH(2''); AAC(6'),yes +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,,N-acetyltransferase domain-containing protein,447,554,1000,,10.88545362392296,, +extracted1,AAAATACACTCAAAGGCATTGAATGTATTTACGCTCTATATAAAAAGAACCGCAGATCTCTTCAGATCTACGGATTTTCGCCATGCCACGAAATTAGGGATATGTTAGCCAGTTAAGGGAACAACGACATGATAAAATGGTAGTTAGCTATATTTTTCTAACTTTGCAACAGAACCCCTAAAAAAAATTCAAAATCTTTCAGAGAAGCTGTTAAAGGAATTTTTAAGTTCACAGATATTAACTTAGCGCGTGAGGCTAAAAATCGATTGATTCATGATTATATCGATCAACCAAAATATTCAAAAGCTTGCGCATCATTGGATGATGGATTCGAAGACGCCTTTCAATATACCGTACAAGGAAATTCCCACAATCGACTAAAGAGTACCAATCTAATTGAACGACTGAATCAAGAAGTACGCAGAAGAGAAAAGATTATTCGCATCTTCCCCAATCAAACATCAGCCAATCGCTTAATTGGAGCCGTTCTTATGGACCTACATGATGAATGGATTTATTCTTCAAGAAAATACATCAATTTTGATAAGTAGAAATGGTAAAAACATTGTATAGCATTTTACACAGGAGTCTGGACTTGACTGAGTTTATGGAAGAAGTTTTAATTGATGATAATATGGTTTTTGATATTGATAATTTAAAAGGATTTCTTAATGATACCAGTTCATTTGGGTTTATAGCTAAAGAAAATAATAAAATTATAGGATTTGCATATTGCTATACACTTTTAAGACCTGATGGAAAAACAATGTTTTATTTACACTCAATAGGAATGTTACCTAACTATCAAGACAAAGGTTATGGTTCAAAATTATTATCTTTTATTAAGGAATATTCTAAAGAGATTGGTTGTTCTGAAATGTTTTTAATAACTGATAAAGGTAATCCTAGAGCTTGCCATGTATATGAAAAATTAGGTGGTAAAAATGATTATAAAGATGAAATAGTATATGTATATGATTATGAAAAAGGTGATAAATAAatgaatatagttgaaaatgaaatatgtataagaactttaatagatgatgattttcctttgatgttaaaatggttaactgatgaaagagtattagaattttatggtggtagagataaaaaatatacattagaatcattaaaaaaacattatacagagccttgggaagatgaagtttttagagtaattattgaatataacaatgttcctattggatatggacaaatatataaaatgtatgatgagttatatactgattatcattatccaaaaactgatgagatagtctatggtatggatcaatttataggagagccaaattattggagtaaaggaattggtacaagatatattaaattgatttttgaatttttgaaaaaagaaagaaatgctaatgcagttattttagaccctcataaaaataatccaagagcaataagggcataccaaaaatctggttttagaattattgaagatttgccagaacatgaattacacgagggcaaaaaagaagattgttatttaatggaatatagatatgatgataatgccacaaatgttaaggcaatgaaatatttaattgagcattactttgataatttcaaagtagatagtattgaaataatcggtagtggttatgatagtgtggcatatttagttaataatgaatacatttttaaaacaaaatttagtactaataagaaaaaaggttatgcaaaagaaaaagcaatatataattttttaaatacaaatttagaaactaatgtaaaaattcctaatattgaatattcgtatattagtgatgaattatctatactaggttataaagaaattaaaggaacttttttaacaccagaaatttattctactatgtcagaagaagaacaaaatttgttaaaacgagatattgccagttttttaagacaaatgcacggtttagattatacagatattagtgaatgtactattgataataaacaaaatgtattagaagagtatatattgttgcgtgaaactatttataatgatttaactgatatagaaaaagattatatagaaagttttatggaaagactaaatgcaacaacagtttttgagggtaaaaagtgtttatgccataatgattttagttgtaatcatctattgttagatggcaataatagattaactggaataattgattttggagattctggaattatagatgaatattgtgattttatatacttacttgaagatagtgaagaagaaataggaacaaattttggagaagatatattaagaatgtatggaaatatagatattgagaaagcaaaagaatatcaagatatagttgaagaatattatcctattgaaactattgtttatggaattaaaaatattaaacaggaatttatcgaaaatggtagaaaagaaatttataaaaggacttataaagattgaTTATATAATATATGAAAAGCTATTATAAAAGACATTAGTATTAAATAGTTTAAAAAAATGAAAAATAATAAAGGAAGTGAGTCAAGTCCAGACTCCTGTGTAAAATGCTATACAATGTTTTTACCATTTCTACTTATCAAAATTGATGTATTTTCTTGAAGAATAAATCCATTCATCATGTAGGTCCATAAGAACGGCTCCAATTAAGCGATTGGCTGATGTTTGATTGGGGAAGATGCGAATAATCTTTTCTCTTCTGCGTACTTCTTGATTCAGTCGTTCAATTAGATTGGTACTCTTTAGTCGATTGTGGGAATTTCCTTGTACGGTATATTGAAAGGCGTCTTCGAATCCATCATCCAATGATGCGCAAGCTTTTGAATATTTTGGTTGATCGATATAATCATGAATCAATCGATTTTTAGCCTCACGCGCTAAGTTAATATCTGTGAACTTAAAAATTCCTTTAACAGCTTCTCTGAAAGATTTTGAATTTTTTTTAGGGGTTCTGTTGCAAAGTTAGAAAAATATAGCTAACTACCATTTTATCATGTCGTTGTTCCCTTAACTGGCTAACATATCCCTAATTTCGTGGCATGGCGAAAATCCGTAGATCTGAAGAGATCTGCGGTTCTTTTTATATAGAGCGTAAATACATTCAATGCCTTTGAGTGTATTTTTTGCCGTATTGATACTTTGATATCTTGTCTTTCTTACTTTAATATGACGGTGATCTTGCTCAATGAGGTTATTCAGATATTTCGATGTACAATGACAGTCAGGTTTAAGTTTAAAAGCTTTAATTACTTTAGCTATTGCTACTTTCGTTGAAGGTGCCTGATCTGTAATTACCTTTTGAGGTTTACCAAATTGTTTAATGAGACGTTTGATAAACGCATATGCTGAATGATTATCTCGTTGCTTACGCAACCAAATATCTAATGTATGTCCCTCTGCATCAATGGCACGATATAAATAGCTCCATTTTCCTTTTATTTTG,3440,AAC(6')-Ie-APH(2'')-Ia,bifunctional aminoglycoside N-acetyltransferase AAC(6')-Ie/aminoglycoside O-phosphotransferase APH(2'')-Ia,1440,1001,2440,Perfect,10.88545362392296,APH(2''); AAC(6'),yes diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/annotation_detail_ANT9-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/annotation_detail_ANT9-Ia.csv index 988c439..9d1b18a 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/annotation_detail_ANT9-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/annotation_detail_ANT9-Ia.csv @@ -1,5 +1,5 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,456,11,466,,12.603822917195512,, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,378,473,850,,12.603822917195512,, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,1001,1783,Perfect,12.603822917195512,ANT(9),yes -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,2640,1909,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase, +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,456,11,466,,12.603822917195512,, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,378,473,850,,12.603822917195512,, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,1001,1783,Perfect,12.603822917195512,ANT(9),yes +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,2640,1909,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase, diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl index 9c2f526..f74454e 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl @@ -14,7 +14,7 @@ CC DOI: 10.1099/mgen.0.000685 CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 07/05/2023, 15:49:09 +CC Annotation Date :: 08/31/2023, 19:06:00 CC CDSs :: 4 CC tRNAs :: 0 CC tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.faa b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.faa rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.ffn b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.ffn similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.ffn rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.ffn diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.fna b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.fna similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.fna rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.fna diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff index 7b2353a..240e79c 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff @@ -1,4 +1,4 @@ -LOCUS contig_1 2783 bp DNA linear UNK 05-JUL-2023 +LOCUS contig_1 2783 bp DNA linear UNK 31-AUG-2023 DEFINITION contig_1, whole genome shotgun sequence. ACCESSION contig_1 VERSION contig_1 @@ -13,7 +13,7 @@ COMMENT Annotated with Bakta URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 07/05/2023, 15:49:09 + Annotation Date :: 08/31/2023, 19:06:00 CDSs :: 4 tRNAs :: 0 tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gff3 b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gff3 similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gff3 rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gff3 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.faa b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.faa rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.tsv b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.tsv rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json index 29afedc..29a8ae6 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json @@ -178,8 +178,8 @@ } ], "run": { - "start": "2023-07-05 15:48:53", - "end": "2023-07-05 15:49:09" + "start": "2023-08-31 19:05:46", + "end": "2023-08-31 19:06:00" }, "version": { "bakta": "1.8.1", diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.tsv b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.tsv rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.txt b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.txt similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.txt rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.txt diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/coverage_annotation_30_ANT9-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/coverage_annotation_30_ANT9-Ia.csv index 436820c..4f3a201 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/coverage_annotation_30_ANT9-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/coverage_annotation_30_ANT9-Ia.csv @@ -1,5 +1,5 @@ -seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,12.603822917195512,456,11,466, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,12.603822917195512,378,473,850, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,12.603822917195512,783,1001,1783,yes -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,12.603822917195512,732,2640,1909, +seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,12.603822917195512,456,11,466, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,12.603822917195512,378,473,850, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,12.603822917195512,783,1001,1783,yes +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,12.603822917195512,732,2640,1909, diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/gene_comparison_30_ANT9-Ia.png b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/gene_comparison_30_ANT9-Ia.png index 91a2bbe..04374de 100644 Binary files a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/gene_comparison_30_ANT9-Ia.png and b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/gene_comparison_30_ANT9-Ia.png differ diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.json b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.json similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.json rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.json diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt rename to test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt index 739e5dd..d32a414 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-49.txt +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-06.txt @@ -1,3 +1,3 @@ -ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note -KIGIOP_00015 aminoglycoside nucleotidyltransferase ANT(9)-Ia Perfect 450 526.939 ANT(9)-Ia 100.0 3002630 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation ANT(9) MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN 100.00 gnl|BL_ORD_ID|1302|hsp_num:0 1386 -KIGIOP_00020 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) Perfect 400 496.508 ErmA 100.0 3000347 protein homolog model n/a n/a macrolide antibiotic; lincosamide antibiotic; streptogramin antibiotic antibiotic target alteration Erm 23S ribosomal RNA methyltransferase MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH 100.00 gnl|BL_ORD_ID|932|hsp_num:0 985 +ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note +KIGIOP_00015 aminoglycoside nucleotidyltransferase ANT(9)-Ia Perfect 450 526.939 ANT(9)-Ia 100.0 3002630 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation ANT(9) MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN 100.00 gnl|BL_ORD_ID|1302|hsp_num:0 1386 +KIGIOP_00020 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) Perfect 400 496.508 ErmA 100.0 3000347 protein homolog model n/a n/a macrolide antibiotic; lincosamide antibiotic; streptogramin antibiotic antibiotic target alteration Erm 23S ribosomal RNA methyltransferase MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH 100.00 gnl|BL_ORD_ID|932|hsp_num:0 985 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/trimmed_annotation_info_ANT9-Ia.csv b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/trimmed_annotation_info_ANT9-Ia.csv index 988c439..9d1b18a 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/trimmed_annotation_info_ANT9-Ia.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ANT9-Ia_1000/trimmed_annotation_info_ANT9-Ia.csv @@ -1,5 +1,5 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,456,11,466,,12.603822917195512,, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,378,473,850,,12.603822917195512,, -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,1001,1783,Perfect,12.603822917195512,ANT(9),yes -extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,2640,1909,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase, +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,456,11,466,,12.603822917195512,, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,,hypothetical protein,378,473,850,,12.603822917195512,, +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,1001,1783,Perfect,12.603822917195512,ANT(9),yes +extracted1,TAACAACGGGATGCCCCAGCATATTGTGCAGAAATTTTTGGGGCATGAAAGCCCAGAAATGACAAGCAGATACGCTCATATCTTTGATGAAACTCTAAAAAATGAATTTACTAAATTTCAGGAAAAACTGGTTACCAATAATGGAGATGTGCTTGATCTAGATGAAGATAATGAAGTCGATGATGTAGAGCTTCAATGGTTCAAGAAAAATATAAATGCACAAGTGCTTCCAAATGGTTATTGTAGATTGCCAGTAGTAGCAGGTGGTTGTCCACATGCGAATGCATGCTTAGATTGCACTCACTTCTGTACCAGTAAGCAATTCTTACCACAGCACGAAGAACAGTTAGAGCGTACAGAAGAGTTATTAGCCATAGCTAAGGATAAACAATGGCAAAGACAAGTAGAGACTAATAGCCGTGTTAAAGAGCGTTTAGAACAAATCATTGGAAGTTTGACGGGGTAATTATCAATGGATAAACAAGTTAGAAATACAACAGAAATTGTACGTTTGGCGAAGCAGAAATCAAAAAAGACAAGGGAAAAAGTAGACAAAGCGATTTCTAAATTTTCGATTGAAGGTAAAGTTATTAATTTTAATTCAATAGCAAAGGAAGCTAATGTTTCTAAATCATGGCTTTATAAGGAACACGATATTAGGCAAAGAATCGAATCCCTTCGTGAGCGTCAAATAACAGCAAATGTAGTCTCAAAACCCAAGAAAAGTTCTCGTTCGGAGGAAATCCTTATTAAAACCTTAAAAAGAAGAGTAATGGAATTAGAAAAAGAAAATAAAAAATTACAGAACCAAATTCAAAAATTATATGGAGATCTGTATAATAAAGAATAATTATTAATCTGTAGACAAATTGTGAAAGGATGTACTTAAACGCTAACGGTCAGCTTTATTGAACAGTAATTTAAGTATATGTCCAATCTAGGGTAAGTAAATTGAGTATCAATATAAACTTTATATGAACATAATCAACGAGGTGAAATCatgagcaatttgattaacggaaaaataccaaatcaagcgattcaaacattaaaaatcgtaaaagatttatttggaagttcaatagttggagtatatctatttggttcagcagtaaatggtggtttacgcattaacagcgatgtagatgttctagtcgtcgtgaatcatagtttacctcaattaactcgaaaaaaactaacagaaagactaatgactatatcaggaaagattggaaatacggattctgttagaccacttgaagttacggttataaataggagtgaagttgtcccttggcaatatcctccaaaaagagaatttatatacggtgagtggctcaggggtgaatttgagaatggacaaattcaggaaccaagctatgatcctgatttggctattgttttagcacaagcaagaaagaatagtatttctctatttggtcctgattcttcaagtatacttgtctccgtacctttgacagatattcgaagagcaattaaggattctttgccagaactaattgaggggataaaaggtgatgagcgtaatgtaattttaaccctagctcgaatgtggcaaacagtgactactggtgaaattacctcgaaagatgtcgctgcagaatgggctatacctcttttacctaaagagcatgtaactttactggatatagctagaaaaggctatcggggagagtgtgatgataagtgggaaggactatattcaaaggtgaaagcactcgttaagtatatgaaaaattctatagaaacttctctcaattagGCTAATTTTATTGCAATAACAGGTGCTTACTTTTAAAACTACTGATTTATTGATAAATATTGAACAATTTTTGGGAAGAATAAAGCGTCCTCTTGTGAAATTAGAGAACGCTTTATTACTTTAATTTAGTGAAACAATTTGTAACTATTGAAAATAGAAAGAAATTGTTCCTTCGATAGTTTATTAATATTAGTGACATTTGCATGCTTCAAAGCCTGTCGGAATTGGTTTTTAGTGAAAAGAACACGATATTCACGGTTTACCCACTTATAAACAAAAGATCGATACTTTTTGTAGTCCTTCTTTGAAATCAATGGTTGATGTCGTTCAAGAACAATCAATACAGAGTCTACACTTGGCTTAGGATGAAAATATAGTGGTGGTACTTTTTTGAGCATTTTTATATCCATCTCCACCATTAATAGTAAACCCAAAGCTCGTTGCAGATTTTGCAATCTTTTCGCAAATCCCTTCTCAACGATAAGATAGCTATATTTAGCCTGACTTTCAAAGGTAATTCTTTTGACAATATCCGTACTGATGTTATAAGGAATATTACCATATATCTTATAGTTTATATGTTTTGGGAAGGAAAATTTTAGAATATCCGTTTGAATCACTTTTATATTCTCAGAGGGGTTTACCGCTTCTTTAGTCACTTGACATAAGCCTCCATCAATTTCTATAGCAGTAACTGATCGACTCATTTTGACTAGCTCTTTGGTAAAATGTCCTTTTCCTGATCCGATTTCTATTACGTTGTCTTGTTTACTGATATTCGTGTGATTCAATATTTCTTTTACATGCTTTTTAGAAGTAATAAAATTTTGCGTGTCTTTAGGGTTTTTCTGGTTCATTATAACCTTCTCCTTACTGGTTCATTATAACCTTCTCCTTACTGGTTATAATGAACTGACATTAAGCGTTCATTATAACCAATTAATTTTGATTTGGTTGATAACGAACTTTATTAATAACAAATATAGAAAAAGTACCCATA,2783,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,2640,1909,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase, diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/annotation_detail_ErmA.csv b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/annotation_detail_ErmA.csv index d28624f..5adc5eb 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/annotation_detail_ErmA.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/annotation_detail_ErmA.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,1001,1732,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase,yes -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,2640,1858,Perfect,12.603822917195512,ANT(9), +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,1001,1732,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase,yes +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,2640,1858,Perfect,12.603822917195512,ANT(9), diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl index fe2f548..9dd9d7b 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.embl +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.embl @@ -14,7 +14,7 @@ CC DOI: 10.1099/mgen.0.000685 CC URL: github.com/oschwengers/bakta CC CC ##Genome Annotation Summary:## -CC Annotation Date :: 07/05/2023, 15:48:26 +CC Annotation Date :: 08/31/2023, 19:05:40 CC CDSs :: 2 CC tRNAs :: 0 CC tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.faa b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.faa rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.ffn b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.ffn similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.ffn rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.ffn diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.fna b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.fna similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.fna rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.fna diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff similarity index 98% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff index 268220d..84e2b7d 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gbff +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gbff @@ -1,4 +1,4 @@ -LOCUS contig_1 2732 bp DNA linear UNK 05-JUL-2023 +LOCUS contig_1 2732 bp DNA linear UNK 31-AUG-2023 DEFINITION contig_1, whole genome shotgun sequence. ACCESSION contig_1 VERSION contig_1 @@ -13,7 +13,7 @@ COMMENT Annotated with Bakta URL: github.com/oschwengers/bakta ##Genome Annotation Summary:## - Annotation Date :: 07/05/2023, 15:48:26 + Annotation Date :: 08/31/2023, 19:05:40 CDSs :: 2 tRNAs :: 0 tmRNAs :: 0 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gff3 b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gff3 similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.gff3 rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.gff3 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.faa b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.faa similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.faa rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.faa diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.tsv b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.hypotheticals.tsv rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.hypotheticals.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json index d418dc1..62a8807 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.json +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.json @@ -130,8 +130,8 @@ } ], "run": { - "start": "2023-07-05 15:48:14", - "end": "2023-07-05 15:48:26" + "start": "2023-08-31 19:05:31", + "end": "2023-08-31 19:05:40" }, "version": { "bakta": "1.8.1", diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.tsv b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.tsv similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.tsv rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.tsv diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.txt b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.txt similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_38685_2023-07-05_15-48/neighbourhood_extracted1.txt rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/bakta_dir_extracted1_1808357_2023-08-31_19-05/neighbourhood_extracted1.txt diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/coverage_annotation_30_ErmA.csv b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/coverage_annotation_30_ErmA.csv index 3c53cb6..010fc2e 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/coverage_annotation_30_ErmA.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/coverage_annotation_30_ErmA.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,12.603822917195512,732,1001,1732,yes -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,12.603822917195512,783,2640,1858, +seq_name,seq_value,seq_length,gene,coverage,length,start_pos,end_pos,target_amr +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,12.603822917195512,732,1001,1732,yes +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,12.603822917195512,783,2640,1858, diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/gene_comparison_30_ErmA.png b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/gene_comparison_30_ErmA.png index 7eb9679..cda1610 100644 Binary files a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/gene_comparison_30_ErmA.png and b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/gene_comparison_30_ErmA.png differ diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-48.json b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-05.json similarity index 100% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-48.json rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-05.json diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-48.txt b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-05.txt similarity index 99% rename from test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-48.txt rename to test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-05.txt index a14d05a..7d7bdfc 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-07-05_15-48.txt +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/rgi_dir/rgi_output_extracted1_2023-08-31_19-05.txt @@ -1,3 +1,3 @@ -ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note -NFDPJF_00005 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) Perfect 400 496.508 ErmA 100.0 3000347 protein homolog model n/a n/a macrolide antibiotic; lincosamide antibiotic; streptogramin antibiotic antibiotic target alteration Erm 23S ribosomal RNA methyltransferase MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH 100.00 gnl|BL_ORD_ID|932|hsp_num:0 985 -NFDPJF_00010 aminoglycoside nucleotidyltransferase ANT(9)-Ia Perfect 450 526.939 ANT(9)-Ia 100.0 3002630 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation ANT(9) MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN 100.00 gnl|BL_ORD_ID|1302|hsp_num:0 1386 +ORF_ID Contig Start Stop Orientation Cut_Off Pass_Bitscore Best_Hit_Bitscore Best_Hit_ARO Best_Identities ARO Model_type SNPs_in_Best_Hit_ARO Other_SNPs Drug Class Resistance Mechanism AMR Gene Family Predicted_DNA Predicted_Protein CARD_Protein_Sequence Percentage Length of Reference Sequence ID Model_ID Nudged Note +NFDPJF_00005 23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A) Perfect 400 496.508 ErmA 100.0 3000347 protein homolog model n/a n/a macrolide antibiotic; lincosamide antibiotic; streptogramin antibiotic antibiotic target alteration Erm 23S ribosomal RNA methyltransferase MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH MNQKNPKDTQNFITSKKHVKEILNHTNISKQDNVIEIGSGKGHFTKELVKMSRSVTAIEIDGGLCQVTKEAVNPSENIKVIQTDILKFSFPKHINYKIYGNIPYNISTDIVKRITFESQAKYSYLIVEKGFAKRLQNLQRALGLLLMVEMDIKMLKKVPPLYFHPKPSVDSVLIVLERHQPLISKKDYKKYRSFVYKWVNREYRVLFTKNQFRQALKHANVTNINKLSKEQFLSIFNSYKLFH 100.00 gnl|BL_ORD_ID|932|hsp_num:0 985 +NFDPJF_00010 aminoglycoside nucleotidyltransferase ANT(9)-Ia Perfect 450 526.939 ANT(9)-Ia 100.0 3002630 protein homolog model n/a n/a aminoglycoside antibiotic antibiotic inactivation ANT(9) MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN MSNLINGKIPNQAIQTLKIVKDLFGSSIVGVYLFGSAVNGGLRINSDVDVLVVVNHSLPQLTRKKLTERLMTISGKIGNTDSVRPLEVTVINRSEVVPWQYPPKREFIYGEWLRGEFENGQIQEPSYDPDLAIVLAQARKNSISLFGPDSSSILVSVPLTDIRRAIKDSLPELIEGIKGDERNVILTLARMWQTVTTGEITSKDVAAEWAIPLLPKEHVTLLDIARKGYRGECDDKWEGLYSKVKALVKYMKNSIETSLN 100.00 gnl|BL_ORD_ID|1302|hsp_num:0 1386 diff --git a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/trimmed_annotation_info_ErmA.csv b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/trimmed_annotation_info_ErmA.csv index d28624f..5adc5eb 100644 --- a/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/trimmed_annotation_info_ErmA.csv +++ b/test/expected_output/annotations/annotations_1000/annotation_ErmA_1000/trimmed_annotation_info_ErmA.csv @@ -1,3 +1,3 @@ -seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,1001,1732,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase,yes -extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,2640,1858,Perfect,12.603822917195512,ANT(9), +seq_name,seq_value,seq_length,gene,product,length,start_pos,end_pos,RGI_prediction_type,coverage,family,target_amr +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ErmA,23S rRNA (adenine(2058)-N(6))-methyltransferase Erm(A),732,1001,1732,Perfect,12.603822917195512,Erm 23S ribosomal RNA methyltransferase,yes +extracted1,AAAAACTCTTGGATTGCCCCTAATTTATAAACATAGGTAGGCGGTGTCTCGACTTCAGATACATTATCAAGAATAACTATTCTTCCTTCCTCATTCAACAGTTCCTTCATTTGCTGTATTACGCTGGCTATATCATCCAAATGATGAAAGGTTGTTCGGCTTACAATAAAATCAAACTTCTCATTAAAATTAAGTTGTTCTGCATTCATATTCAGATAGACCGTATTTGTTAGTTGACGTTTAGATTTGGCAAGATCGAGCATTTGATTAGAAATATCAATCCCTACCACTTCATCATAATAACTTGCTAATTTCTCCACTAACAAACCCGAGCCACATCCGATATCTAATGCTCTGCCTTTCTTTGGAGACATATTAGACACAAAGAATGAATAATCATTCAAAAGCTCATTCACGAAATCGTAATCTTCTGCAACCTTATCAAACTGTGATTCTATTGTATTCAAAAAGATCCCCCATTCCTACTTTATCGACATTCTTTCATTACTTACCACTTTAGATGTTTTTTCGTTGGGGATAAAACTTCCCTTTAGACAATTTTATCCAAAGACAATACAACAGTGCAACTTTATTAAAGTCACTGTCCTTTATCGCAGCCTTTACTTTTTAGTAAAGACAGTGGCTTCTCTTATCAAGTTTCAAAACATATTATTTTGAAGAAAACGTCCATCTGAAGTGTCAAGTGCAAAATTACATATAAAGGTTTATTCTAAAATGAAAAGATGATACAATCATATTCAGTTACATAAGGAGGTTTCAATTATGTGCACCAGTATCGCAGTAGTAGAAATTACTTTATCTCATTCATAATGAAAAAAATGGAAAGGAGATAAAAGTATGGGTACTTTTTCTATATTTGTTATTAATAAAGTTCGTTATCAACCAAATCAAAATTAATTGGTTATAATGAACGCTTAATGTCAGTTCATTATAACCAGTAAGGAGAAGGTTATAATGAACCAGTAAGGAGAAGGTTATAatgaaccagaaaaaccctaaagacacgcaaaattttattacttctaaaaagcatgtaaaagaaatattgaatcacacgaatatcagtaaacaagacaacgtaatagaaatcggatcaggaaaaggacattttaccaaagagctagtcaaaatgagtcgatcagttactgctatagaaattgatggaggcttatgtcaagtgactaaagaagcggtaaacccctctgagaatataaaagtgattcaaacggatattctaaaattttccttcccaaaacatataaactataagatatatggtaatattccttataacatcagtacggatattgtcaaaagaattacctttgaaagtcaggctaaatatagctatcttatcgttgagaagggatttgcgaaaagattgcaaaatctgcaacgagctttgggtttactattaatggtggagatggatataaaaatgctcaaaaaagtaccaccactatattttcatcctaagccaagtgtagactctgtattgattgttcttgaacgacatcaaccattgatttcaaagaaggactacaaaaagtatcgatcttttgtttataagtgggtaaaccgtgaatatcgtgttcttttcactaaaaaccaattccgacaggctttgaagcatgcaaatgtcactaatattaataaactatcgaaggaacaatttctttctattttcaatagttacaaattgtttcactaaATTAAAGTAATAAAGCGTTCTCTAATTTCACAAGAGGACGCTTTATTCTTCCCAAAAATTGTTCAATATTTATCAATAAATCAGTAGTTTTAAAAGTAAGCACCTGTTATTGCAATAAAATTAGCCTAATTGAGAGAAGTTTCTATAGAATTTTTCATATACTTAACGAGTGCTTTCACCTTTGAATATAGTCCTTCCCACTTATCATCACACTCTCCCCGATAGCCTTTTCTAGCTATATCCAGTAAAGTTACATGCTCTTTAGGTAAAAGAGGTATAGCCCATTCTGCAGCGACATCTTTCGAGGTAATTTCACCAGTAGTCACTGTTTGCCACATTCGAGCTAGGGTTAAAATTACATTACGCTCATCACCTTTTATCCCCTCAATTAGTTCTGGCAAAGAATCCTTAATTGCTCTTCGAATATCTGTCAAAGGTACGGAGACAAGTATACTTGAAGAATCAGGACCAAATAGAGAAATACTATTCTTTCTTGCTTGTGCTAAAACAATAGCCAAATCAGGATCATAGCTTGGTTCCTGAATTTGTCCATTCTCAAATTCACCCCTGAGCCACTCACCGTATATAAATTCTCTTTTTGGAGGATATTGCCAAGGGACAACTTCACTCCTATTTATAACCGTAACTTCAAGTGGTCTAACAGAATCCGTATTTCCAATCTTTCCTGATATAGTCATTAGTCTTTCTGTTAGTTTTTTTCGAGTTAATTGAGGTAAACTATGATTCACGACGACTAGAACATCTACATCGCTGTTAATGCGTAAACCACCATTTACTGCTGAACCAAATAGATATACTCCAACTATTGAACTTCCAAATAAATCTTTTACGATTTTTAATGTTTGAATCGCTTGATTTGGTATTTTTCCGTTAATCAAATTGCTCATGATTTCACCTCGTTGATTATGTTCATATAAAGTTTATATTGATACTCAATTTACTTACCCTAGATTGGACATATACTTAAATTACTGTTCAA,2732,ANT(9)-Ia,aminoglycoside nucleotidyltransferase ANT(9)-Ia,783,2640,1858,Perfect,12.603822917195512,ANT(9), diff --git a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-07-05_15-48.csv b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-08-31_19-05.csv similarity index 97% rename from test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-07-05_15-48.csv rename to test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-08-31_19-05.csv index ad4264d..93426b1 100644 --- a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-07-05_15-48.csv +++ b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-08-31_19-05.csv @@ -1,10 +1,10 @@ -sequence,node,coverage,start,end -1,49,39.346733668341706,0,120 -1,57,29.934117647058823,121,545 -1,519,10.88545362392296,546,999 -1,519,10.88545362392296,1000,2439 -1,519,10.88545362392296,2440,2573 -1,57,29.934117647058823,2574,2998 -1,49,39.346733668341706,2999,3197 -1,39,55.94818652849741,3198,3390 -1,23,27.133928571428573,3391,3439 +sequence,node,coverage,start,end +1,49,39.346733668341706,0,120 +1,57,29.934117647058823,121,545 +1,519,10.88545362392296,546,999 +1,519,10.88545362392296,1000,2439 +1,519,10.88545362392296,2440,2573 +1,57,29.934117647058823,2574,2998 +1,49,39.346733668341706,2999,3197 +1,39,55.94818652849741,3198,3390 +1,23,27.133928571428573,3391,3439 diff --git a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-07-05_15-48.csv b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-08-31_19-05.csv similarity index 97% rename from test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-07-05_15-48.csv rename to test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-08-31_19-05.csv index 55f0dd8..b4251fd 100644 --- a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-07-05_15-48.csv +++ b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ANT9-Ia_1000_2023-08-31_19-05.csv @@ -1,4 +1,4 @@ -sequence,node,coverage,start,end -1,127,12.603822917195512,0,999 -1,127,12.603822917195512,1000,1782 -1,127,12.603822917195512,1783,2782 +sequence,node,coverage,start,end +1,127,12.603822917195512,0,999 +1,127,12.603822917195512,1000,1782 +1,127,12.603822917195512,1783,2782 diff --git a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-07-05_15-48.csv b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-08-31_19-05.csv similarity index 97% rename from test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-07-05_15-48.csv rename to test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-08-31_19-05.csv index fcbcff3..ab703c9 100644 --- a/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-07-05_15-48.csv +++ b/test/expected_output/sequences_info/sequences_info_1000/paths_info/ng_sequences_ErmA_1000_2023-08-31_19-05.csv @@ -1,4 +1,4 @@ -sequence,node,coverage,start,end -1,127,12.603822917195512,0,999 -1,127,12.603822917195512,1000,1731 -1,127,12.603822917195512,1732,2731 +sequence,node,coverage,start,end +1,127,12.603822917195512,0,999 +1,127,12.603822917195512,1000,1731 +1,127,12.603822917195512,1732,2731 diff --git a/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-07-05_15-48.txt b/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-08-31_19-05.txt similarity index 100% rename from test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-07-05_15-48.txt rename to test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_AAC6SS-Ie-APH2SSSS-Ia_1000_2023-08-31_19-05.txt diff --git a/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ANT9-Ia_1000_2023-07-05_15-48.txt b/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ANT9-Ia_1000_2023-08-31_19-05.txt similarity index 100% rename from test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ANT9-Ia_1000_2023-07-05_15-48.txt rename to test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ANT9-Ia_1000_2023-08-31_19-05.txt diff --git a/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ErmA_1000_2023-07-05_15-48.txt b/test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ErmA_1000_2023-08-31_19-05.txt similarity index 100% rename from test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ErmA_1000_2023-07-05_15-48.txt rename to test/expected_output/sequences_info/sequences_info_1000/sequences/ng_sequences_ErmA_1000_2023-08-31_19-05.txt