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CHANGELOG.md

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Change Log

All notable changes to this project will be documented in this file. This project adheres to Semantic Versioning.

[0.5.1] - 2020-10-21

Fixed

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

[0.5] - 2020-06-03

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).

[0.4] - 2020-04-09

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).

[0.3.3] - 2017-06-21

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.

[0.3.2] - 2017-04-19

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.

[0.3.1] - 2017-02-02

Fixed

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

[0.3.0] - 2017-02-02

Added

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

[0.2.0] - 2017-01-18

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.

[0.1.1] - 2016-12-19

Changed

  • CLI implemented using entry_points instead of a dedicated script.

Fixed

  • Entry type inference now correct by inheriting from object.

[0.1.0] - 2016-12-16

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