tag v0.5.1

Fixed

• A bug with handling of the "Parent" attribute for features with multiple parents (see #85).

tag v0.5

Added

• New NamedIndex class for storing and retrieving features by ID (see #82).
• New CLI command tag pep2nuc for transforming feature coordinates from peptide space to nucleotide space (see #83).

tag v0.4

Added

• New tag.select.merge function to efficiently merge sorted feature streams (see #68).
• New tag.locus module for efficient parsing locus coordinates from multiple annotation streams (see #71).
• New experimental tag.bae module for evaluating bacterial annotation (see #73, #76).

Changed

• Minor updates to compensate for a couple years' worth of neglect (see #64).
• Refactored GFF3Reader to better support processing of unsorted GFF3 data (see #65).
• Implemented finer control of how and when output separator directives (###) are printed to GFF3 output (see #68, #75).
• Reorganized test suite code and data (see #70).
• Refactored the Feature and Score APIs with more sane default and static constructors (see #74).

Fixed

• The GFF3Writer class now behaves as expected when .retainids is set to True (see #79).

tag v0.3.3

Fixed

• Missing extent query from the index implementation.
• Aliased index.keys() to index.seqids.

Added

• Script tag sum to provide very basic summaries of genomic GFF3 files.

tag v0.3.2

Added

• Pseudo-features for better handling and sorting of top-level multi-features.
• A new primary_transcript filter as a generalization of the primary_mrna
  function.
• A new function to query features for NCBI GeneID values.
• A new function to traverse a feature and all of its children to collect all
  attribute values associate with a given key.

Fixed

• Bug with non-protein coding genes and the tag.mrna.primary filter (now
  primary_mrna in the tag.transcript module).
• Bug with how the GFF3 writer handles multi-feature IDs.

Changed

• Refactored the mrna module, extended it, and renamed it to transcript to
  reflect its new and broader scope.

tag v0.3.1

Fixed

• Range overlap queries accidentally left out of the previous release.

tag v0.3.0

Added

• New convenience functions in the Range and Feature classes for range and
  point overlap queries.

tag v0.2.0

Added

• An index class for efficient in-memory access of sequence features.
• Module for mRNA handling, with a function for selecting the primary mRNA from
  a gene or other feature.
• New CLI command tag pmrna.
• A new Score class for internal handling of feature scores. Not yet included
  in the API, and may not ever be.

Changed

• Modules focused on classes / data structure now support more concise imports
  (for example, from tag import Feature and tag.Feature now supported and
  preferred over from tag.feature import feature and tag.feature.Feature).

Fixed

• Resolved a bug with the GFF3Writer failing to print ##FASTA directives
  before writing sequences to output.

tag v0.1.1

Changed

• CLI implemented using entry_points instead of a dedicated script.

Fixed

• Entry type inference now correct by inheriting from object.

tag v0.1.0

The first stable release of the tag package!

Added

• Basic data structures
  • Range
  • Comment
  • Directive
  • Sequence
  • Feature
• Annotation I/O
  • GFF3Reader
  • GFF3Writer
• Composable generator functions for streaming annotation processing
• A command line interface through the tag script
• Package scaffolding
  • README
  • documentation
  • license
  • changelog
  • various config files