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Release 0.8.1

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@simonvh simonvh released this 11 May 18:03
0.8.1
29b9425

[0.8.1] - 2020-05-11

Added

  • Now using the UCSC rest API
  • genomepy search now accepts taxonomy IDs
  • genomepy search will now return taxonomy IDs and Accession numbers
  • The README.txt will now store taxonomy IDs and Accession numbers
  • Gene annotations:
    • Downloading of annotation file (BED/GTF/GFF3) from URL
    • Automatic search for annotation file (GTF/GFF3) in genome directory when downloading from URL
    • Option for URL provider to link to annotation file (to process is similarly to other providers)
    • Automatic annotation sanitizing (and skip sanitizing flag -s for genomepy install)
    • Option to only download annotation with genomepy install -o
  • Plugins:
    • Blacklists are automatically unzipped.
    • Multithreading support for plugins, thanks to alienzj!
    • STAR now uses the annotation file for a (one-pass) splice-aware index

Changed

  • sizes no longer a plugin, but always gets executed
  • genomepy FUNCTION --help texts expanded
  • all genomepy classes exported when imported into Python
  • all providers now let you know when they are downloading assembly information.
  • more descriptive feedback to installing & many errors

Removed

  • Sizes plugin
  • Old tests
  • Removed outdated dependency xmltodict

Fixed

  • genomepy config options made more robust
  • README.txt will no longer:
    • update 3x for each command
    • drop regex info
    • have duplicate lines

Refactoring

  • Genome class moved to genome.py
  • Many functions moved to utils.py
  • Many other functions made static methods of a class
  • Genome.track2fasta and Genome.get_random_sequence optimized
  • All Provider classes now store their genomes as a dict-in-dict, with the assembly name as key.
  • Many Provider class functions now standardized. Many functions moved to from the daughter classes to the ProviderBase
    class.
  • README.txt file generation and updating standardized
  • Unit tests! all functions now have an individual test. Almost all test use functions already tested prior to them.
  • Old tests incorporated in several extra tests (e01, e02, e03).
  • Raise statements now use more fitting errors
  • All instances of os.remove exchanged for os.unlink
  • Almost all warnings fixed
  • Extensive, COVID19-enabled, and somewhat pointless alphabetizing, optimizing and/or organizing changes to
    • imports everywhere
    • .gitignore
    • .travis.yml
    • release_checklist.md
    • cli.py
    • strings (many strings with .format() replaced with f-strings)
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