Merge pull request #48 from VukManojlovic/CTX-4505

CTX-4505: Added a paired-end demultipleixng and three clustering commands

coretex/bioinformatics/ctx_qiime2/__init__.py

@@ -19,9 +19,9 @@
 from pathlib import Path
 
 from .utils import compressGzip, createSample, getDemuxSamples, getDenoisedSamples, \
-    getFastqDPSamples, getFastqMPSamples, getMetadataSample, getPhylogeneticTreeSamples, \
+    getFastqDPSamples, getFastqMPSamples, getImportedSamples, getMetadata, getPhylogeneticTreeSamples, \
     isDemultiplexedSample, isDenoisedSample, isFastqDPSample, isFastqMPSample, \
-    isMetadataSample, isPhylogeneticTreeSample, sampleNumber
+    isImportedSample, isPhylogeneticTreeSample, sampleNumber, isPairedEnd
 
 from ..utils import command
 
@@ -67,6 +67,55 @@ def demuxEmpSingle(
     ])
 
 
+def demuxEmpPaired(
+    sequencesPath: Union[str, Path],
+    barcodesPath: Union[str, Path],
+    barcodesColumn: str,
+    perSampleSequences: Union[str, Path],
+    errorCorretctionDetailsPath: Union[str, Path]
+) -> None:
+    """
+        Wrapper for QIIME's demux emp-paired command, which performs demultiplexing of multiplexed
+        sequences in the Earth Microbiome Project amplicon sequencing standard format
+        http://www.earthmicrobiome.org/protocols-and-standards/.
+
+        Parameters
+        ----------
+        sequencesPath : Union[str, Path]
+            Path to the paired-end demultiplexed sequences to be denoised
+        barcodesPath : Union[str, Path]
+            Output path to the resulting feature sequences
+        perSampleSequences : Union[str, Path]
+            Output path to the resulting feature table
+        errorCorretctionDetailsPath : Union[str, Path]
+            Output path to the statistics of the denoising
+        multithreading : bool
+            Whether to use multithreading. One thread per CPU core
+    """
+
+    if isinstance(sequencesPath, Path):
+        sequencesPath = str(sequencesPath)
+
+    if isinstance(barcodesPath, Path):
+        barcodesPath = str(barcodesPath)
+
+    if isinstance(perSampleSequences, Path):
+        perSampleSequences = str(perSampleSequences)
+
+    if isinstance(errorCorretctionDetailsPath, Path):
+        errorCorretctionDetailsPath = str(errorCorretctionDetailsPath)
+
+    command([
+        "qiime", "demux", "emp-paired",
+        "--i-seqs", sequencesPath,
+        "--m-barcodes-file", barcodesPath,
+        "--m-barcodes-column", barcodesColumn,
+        "--o-per-sample-sequences", perSampleSequences,
+        "--o-error-correction-details", errorCorretctionDetailsPath,
+        "--verbose"
+    ])
+
+
 def demuxSummarize(dataPath: str, visualizationPath: str) -> None:
     command([
         "qiime", "demux", "summarize",
@@ -111,7 +160,7 @@ def dada2DenoiseSingle(
         denoisingStatsPath : Union[str, Path]
             Output path to the statistics of the denoising
         multithreading : bool
-            Whether to use multithreading
+            Whether to use multithreading. One thread per CPU core
     """
 
     if isinstance(inputPath, Path):
@@ -191,7 +240,7 @@ def dada2DenoisePaired(
         denoisingStatsPath : Union[str, Path]
             Output path to the statistics of the denoising
         multithreading : bool
-            Whether to use multithreading
+            Whether to use multithreading. One thread per CPU core
     """
 
     if isinstance(inputPath, Path):
@@ -453,3 +502,192 @@ def taxaCollapse(
         "--p-level", str(level),
         "--o-collapsed-table", collapsedTablePath
     ])
+
+def vsearchClusterDeNovo(
+    tablePath: Union[str, Path],
+    representativeSequencesPath: Union[str, Path],
+    percIdentity: float,
+    clusteredTablePath: Union[str, Path],
+    clusteredSequencesPath: Union[str, Path],
+    multithreading: bool = True
+) -> None:
+    """
+        Wrapper for QIIME2's vsearch de novo clusteing command.
+
+        Parameters
+        ----------
+        tablePath : Union[str, Path]
+            Path to the feature table generated by DADA2 denoise
+        representativeSequencesPath : Union[str, Path]
+            Path to the represenative sequences generated by DADA2 denoise
+        percIdentity : float
+            Percent identiy threshold for the OTU clustering
+        clusteredTablePath : Union[str, Path]
+            Path to the output clustered feature table
+        clusteredSequencesPath : Union[str, Path]
+            Path to the output clustered sequences
+        multithreading : bool
+            Whether to use multithreading. One thread per CPU core
+    """
+
+    if isinstance(tablePath, Path):
+        tablePath = str(tablePath)
+
+    if isinstance(representativeSequencesPath, Path):
+        representativeSequencesPath = str(representativeSequencesPath)
+
+    if isinstance(clusteredTablePath, Path):
+        clusteredTablePath = str(clusteredTablePath)
+
+    if isinstance(clusteredSequencesPath, Path):
+        clusteredSequencesPath = str(clusteredSequencesPath)
+
+    args = [
+        "qiime", "vsearch", "cluster-features-de-novo",
+        "--i-table", tablePath,
+        "--i-sequences", representativeSequencesPath,
+        "--p-perc-identity", str(percIdentity),
+        "--o-clustered-table", clusteredTablePath,
+        "--o-clustered-sequences", clusteredSequencesPath
+    ]
+
+    if multithreading:
+        args.extend(["--p-threads", "0"])
+
+    command(args)
+
+
+def vsearchClusterClosedReference(
+    tablePath: Union[str, Path],
+    representativeSequencesPath: Union[str, Path],
+    referenceSequencesPath: Union[str, Path],
+    percIdentity: float,
+    clusteredTablePath: Union[str, Path],
+    clusteredSequencesPath: Union[str, Path],
+    unmatchedSequencesPath: Union[str, Path],
+    multithreading: bool = True
+) -> None:
+    """
+        Wrapper for QIIME2's vsearch closed reference clusteing command.
+
+        Parameters
+        ----------
+        tablePath : Union[str, Path]
+            Path to the feature table generated by DADA2 denoise
+        representativeSequencesPath : Union[str, Path]
+            Path to the represenative sequences generated by DADA2 denoise
+        referenceSequencesPath : Union[str, Path]
+            Path to reference OTU sequences
+        percIdentity : float
+            Percent identiy threshold for the OTU clustering
+        clusteredTablePath : Union[str, Path]
+            Path to the output clustered feature table
+        clusteredSequencesPath : Union[str, Path]
+            Path to the output clustered sequences
+        unmatchedSequencesPath : Union[str, Path]
+            Path to the output unmatched sequences
+        multithreading : bool
+            Whether to use multithreading. One thread per CPU core
+    """
+
+    if isinstance(tablePath, Path):
+        tablePath = str(tablePath)
+
+    if isinstance(representativeSequencesPath, Path):
+        representativeSequencesPath = str(representativeSequencesPath)
+
+    if isinstance(referenceSequencesPath, Path):
+        referenceSequencesPath = str(referenceSequencesPath)
+
+    if isinstance(clusteredTablePath, Path):
+        clusteredTablePath = str(clusteredTablePath)
+
+    if isinstance(clusteredSequencesPath, Path):
+        clusteredSequencesPath = str(clusteredSequencesPath)
+
+    if isinstance(unmatchedSequencesPath, Path):
+        unmatchedSequencesPath = str(unmatchedSequencesPath)
+
+    args = [
+        "qiime", "vsearch", "cluster-features-closed-reference",
+        "--i-table", tablePath,
+        "--i-sequences", representativeSequencesPath,
+        "--i-reference-sequences", referenceSequencesPath,
+        "--p-perc-identity", str(percIdentity),
+        "--o-clustered-table", clusteredTablePath,
+        "--o-clustered-sequences", clusteredSequencesPath,
+        "--o-unmatched-sequences", unmatchedSequencesPath
+    ]
+
+    if multithreading:
+        args.extend(["--p-threads", "0"])
+
+    command(args)
+
+
+def vsearchClusterOpenReference(
+    tablePath: Union[str, Path],
+    representativeSequencesPath: Union[str, Path],
+    referenceSequencesPath: Union[str, Path],
+    percIdentity: float,
+    clusteredTablePath: Union[str, Path],
+    clusteredSequencesPath: Union[str, Path],
+    newReferenceSequencesPath: Union[str, Path],
+    multithreading: bool = True
+) -> None:
+    """
+        Wrapper for QIIME2's vsearch open reference clusteing command.
+
+        Parameters
+        ----------
+        tablePath : Union[str, Path]
+            Path to the feature table generated by DADA2 denoise
+        representativeSequencesPath : Union[str, Path]
+            Path to the represenative sequences generated by DADA2 denoise
+        referenceSequencesPath : Union[str, Path]
+            Path to reference OTU sequences
+        percIdentity : float
+            Percent identiy threshold for the OTU clustering
+        clusteredTablePath : Union[str, Path]
+            Path to the output clustered feature table
+        clusteredSequencesPath : Union[str, Path]
+            Path to the output clustered sequences
+        newReferenceSequencesPath : Union[str, Path]
+            Path to the output new reference sequences
+        multithreading : bool
+            Whether to use multithreading. One thread per CPU core
+    """
+
+    if isinstance(tablePath, Path):
+        tablePath = str(tablePath)
+
+    if isinstance(representativeSequencesPath, Path):
+        representativeSequencesPath = str(representativeSequencesPath)
+
+    if isinstance(referenceSequencesPath, Path):
+        referenceSequencesPath = str(referenceSequencesPath)
+
+    if isinstance(clusteredTablePath, Path):
+        clusteredTablePath = str(clusteredTablePath)
+
+    if isinstance(clusteredSequencesPath, Path):
+        clusteredSequencesPath = str(clusteredSequencesPath)
+
+    if isinstance(newReferenceSequencesPath, Path):
+        newReferenceSequencesPath = str(newReferenceSequencesPath)
+
+    args = [
+        "qiime", "vsearch", "cluster-features-open-reference",
+        "--i-table", tablePath,
+        "--i-sequences", representativeSequencesPath,
+        "--i-reference-sequences", referenceSequencesPath,
+        "--p-perc-identity", str(percIdentity),
+        "--o-clustered-table", clusteredTablePath,
+        "--o-clustered-sequences", clusteredSequencesPath,
+        "--o-new-reference-sequences", newReferenceSequencesPath
+    ]
+
+    if multithreading:
+        args.extend(["--p-threads", "0"])
+
+    command(args)