gfftk - GFFtk v25.6.10

Changes

• bump version to 25.6.10 to match git tag (c9e9c12)
• add --grep --grepv filtering to convert (e1959f8)
• add utr_extension in consensus module (d44a61a5aa24a2dfd744ee524a28c6401a18e500)

Full Changelog: https://github.com/nextgenusfs/gfftk/compare/v25.6.9...v25.6.10

- Python
Published by github-actions[bot] 10 months ago

gfftk - GFFtk v25.4.17

• Some modifications to the gfftk consensus module for more accurate evidence based scoring
• Added unit tests and updated linting/formatting.

What's Changed

• Update main.py by @olekto in https://github.com/nextgenusfs/gfftk/pull/6

New Contributors

• @olekto made their first contribution in https://github.com/nextgenusfs/gfftk/pull/6

Full Changelog: https://github.com/nextgenusfs/gfftk/compare/v24.10.30...v25.4.17

- Python
Published by nextgenusfs 12 months ago

gfftk - gfftk v24.10.30

• bug fix release
• improved parsing for some gtf formats

Full Changelog: https://github.com/nextgenusfs/gfftk/compare/v24.2.4...v24.10.30

- Python
Published by nextgenusfs over 1 year ago

gfftk - gfftk v24.2.4

• Upgrade the consensus module, more accurate calls and opposite strand filtering.
• A few bug fixes.

- Python
Published by nextgenusfs about 2 years ago

gfftk - gfftk v23.12.5

Bug fix release:

• fix fasta parser for whitespace #2
• fix genbank cleanup

- Python
Published by nextgenusfs over 2 years ago

gfftk - gfftk v23.9.6

• move to CalVar version system (date)
• update GFF3 parsers
• provide support for genbank flat file output

- Python
Published by nextgenusfs over 2 years ago

gfftk - gfftk v0.1.7

• fix for writing gzip output files

- Python
Published by nextgenusfs over 3 years ago

gfftk - gfftk v0.1.6

• add support for io.BytesIO objects to be used as input -- this won't have an effect on the cli gfftk package, but could benefit as a library if streams are used.

- Python
Published by nextgenusfs over 3 years ago

gfftk - gfftk v0.1.5

• Add support for detecting pseudogenes, ie mRNA features that have CDS with internal stops or those that are previously labeled pseudogenes. Pseudogenes will still be written, however, CDS will not be.
• Add option to gff.gff2dict for gff_format="auto" where the format will try autodetect to parse some different GFF formats. Currently just supports the default and the NCBI-eukaryote format.

- Python
Published by nextgenusfs over 3 years ago

gfftk - gfftk: initial release v0.1.4

Most of this code has pulled out of the funannotate repository to create a separate package/dependency to make the code base easier to maintain. There are some added features here, notably gfftk consensus which is an Evidence-Modeler-like script (still needs a little bit more work to handle some edge cases). This package/library is useful to parse, convert, manipulate genome annotation files (GFF3, TBL, GTF).

- Python
Published by nextgenusfs over 3 years ago