Release 0.8.1

[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• Removed outdated dependency xmltodict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)

Release 0.7.2

[0.7.2] - 2019-03-31

Fixes

• Fix minor issue with hg19 wrong blacklist url
• Ensembl downloads over http instead of https (release 99 no longer has https)

hotfix

[0.7.1] - 2019-11-20

Fixes

• STAR is not longer enabled by default

Release 0.7.0

[0.7.0] - 2019-11-18

Added

• Direct downloading from url through url provider.
• Added --force flag. Files will no longer be overwritten by default.
• Provider specific options:
  • --ensembl-version: specify release version.
  • --ensembl-toplevel: by default, genomepy install will search for primary assemblies.
    This flag will only download toplevel assemblies.
• Added STAR index plugin

Changed

• Providers are now case-insensitive.
• Extended testing.
• Increased minimal Python version to 3.6.
• Removed gaps from plugins, added gaps to core functionality.

Fixed

• bugfix: NCBI will show all versions of an assembly (will no longer filter on BioSample ID, instead filters on asm_name).
• fix: gaps file will be generated when needed.

Release 0.6.1

[0.6.1] - 2019-10-10

Bugfix release

Fixed

• Fixed bug with get_track_type().

Release 0.6.0.

Added

• Support for storing bzgip-compressed genomes (#41).

Changed

• Removed support for Python 2 (2020 is close!).

Fixed

• Ensembl annotation for non-vertebrate genomes should work again.
• Fixed bug where a deleted or empty config file would result in an error.

Release 0.5.5

[0.5.5] - 2019-03-19

Added

• Plugin for downloading genome blacklists (from Kundaje lab).

Fixed

• Fix for new Ensembl REST API and FTP layout.
• Genomes from Ensembl with a space in their name can be downloaded.
• Plugin imports use relative parts to prevent conflicts with other imports.

Release 0.5.4

Added

• Downloading annotation from NCBI now implemented.
• Genbank assemblies at NCBI can be searched and downloaded

Fixed

• Fixed #23.
• Fixed #26.
• Fixed Ensembl downloads (#30)
• Fixed FTP tests for CI

Release 0.5.2

• Fixed genome_dir argument to genomepy install
• Fixed msgpack dependency
• Fixed issue with config generate where config directory does note exist.

Release 0.5.1

Release notes:

• Fixed installation issue with msgpack