Bakta

This is the first v1.4 patch release (v1.4.1) fixing a tiny simple but critical bug causing all imported contigs being treated as complete sequences. A patch upgrade is highly recommended!

Improvements:
- removed trailing asterik chars on AA import https://github.com/oschwengers/bakta/issues/97: https://github.com/oschwengers/bakta/commit/a447f327a4b7344883c1154e12ba7287ff8d86a2
- caught AA bulk annotation import errors https://github.com/oschwengers/bakta/issues/97: https://github.com/oschwengers/bakta/commit/58cedf148a847e946f21f2115b69244eba1cd692

Bug fixes:
- fixed fasta import contig attribute types https://github.com/oschwengers/bakta/issues/108
- fixed dnaA/repA revisions https://github.com/oschwengers/bakta/issues/108 (Thanks conmeehan)

This is the fourth minor release (v1.4) introducing the detection of translational exceptions and protein bulk annotations.

Compatible database scheme version: 3

New features:
- detection & annotation of selenocysteine translational exceptions: 100
- support for protein bulk annotations (direct annotation of proteins w/o genomes): 101 (Thanks conmeehan)

Improvements:
- maintainability improvements like Python type hints code refactorings: 96 https://github.com/oschwengers/bakta/commit/943485c12fc60a0f07f2b72c38dae43c25e21155
- added a large(r) genome test dataset and a corresponding Nextflow script: https://github.com/oschwengers/bakta/commit/32e0f9e847f2b39abef58d3c3e694a4146d03f1e
- add more CI tests: https://github.com/oschwengers/bakta/commit/ce2c68f972029e7b7b11782cb18c5b2fd199f653 https://github.com/oschwengers/bakta/commit/4549f2582ec6f7388fa6f6ad177ea288c1066a1c

Bug fixes:
- fixed molecular weight in hypothetical tsv output https://github.com/oschwengers/bakta/commit/d83c1b8fa1604a98b36710d14c96514150a8e998

And of course all improvements and bug fixes from all v1.3.x patch releases.

This is the third v1.3 patch release (v1.3.3).

This is a quick fix reverting an `alive-progress` version bump to `v2.1.0` that is not available via Conda. Sorry for any inconvenience caused.

Bug fixes:
- fixed a file permission issue on bakta_db update: https://github.com/oschwengers/bakta/commit/de42d3fad5cbe574b6c2b7a643ea246c247a2017
- pinned `alive-progress` version to `v1.6.2` to fix potential API errors: https://github.com/oschwengers/bakta/commit/dbc79acc40b3999da916f2aaa319e2de3c432db0 https://github.com/oschwengers/bakta/commit/60ac3ed02537628bb9264d18e16080e4a9ee5b54

This is the second v1.3 patch release (v1.3.2).

Bug fixes:
- fixed a file permission issue on bakta_db update: https://github.com/oschwengers/bakta/commit/de42d3fad5cbe574b6c2b7a643ea246c247a2017
- bumped alive-progress version to >=v2.1.0 to fix potential API errors: https://github.com/oschwengers/bakta/commit/dbc79acc40b3999da916f2aaa319e2de3c432db0

This is the first v1.3 patch release (v1.3.1).

Bug fixes:
- fixed the locus-tag checks: use a more relaxed format as default and INSDC restrictions on `--compliant`: https://github.com/oschwengers/bakta/commit/e2651c3c7c85efbbceacff1ac28482b3c636b536 (Thanks taylorreiter)
- skip `/pseudo` annotated genes in `--proteins`-provided GenBank files: https://github.com/oschwengers/bakta/commit/0f0165d0909ef26be29477751db301e68754f233 (Thanks Charlotte Reuschel)

This is the third minor release (v1.3) introducing a new feature and many improvements and bug fixes.

Compatible database scheme version: 3

New features:
- prediction of signal peptides via [DeepSig](https://github.com/BolognaBiocomp/deepsig): #32 (Thanks Anna-Rehm)

Improvements:
- provide summary with genome & annotation statistics as `.txt` file: 88 (Thanks hkaspersen)
- accept user provided proteins in GenBank format: 89 (Thanks Tonny-zhou)
- removed alignment gaps (`-`) in input sequences: 87 (Thanks RotimiDada)
- improved sORF overlap filter runtime performance: https://github.com/oschwengers/bakta/commit/cb204fbe52539abd92059b67b08b5f3352dea0b0
- improved outputs: https://github.com/oschwengers/bakta/commit/76e07a4db073bf839a2280e8fad1951d44e6c9e8 https://github.com/oschwengers/bakta/commit/90bfe99c65565036c0943e70fd9daa4d2321f610
- added more checks & tests: https://github.com/oschwengers/bakta/commit/b779e1fda82302e9156af0c1be9a7285e263c21d https://github.com/oschwengers/bakta/commit/4e6c35d3177977e9cec9bcf6cc86116f55cdd590 https://github.com/oschwengers/bakta/commit/f4103f09b7dc6edb49164e82a83a9b931d42eee6 https://github.com/oschwengers/bakta/commit/08ebb037bca1e976d102fe293d775a70b80ebd36 https://github.com/oschwengers/bakta/commit/1672a876141711f22d1cc8dd930a6f397458616d https://github.com/oschwengers/bakta/commit/26a8ed2f30eff456b808f62b0646039f566ff3b7
- added `--gram` to CWL file: https://github.com/oschwengers/bakta/commit/22463196c55bb93f20f6161ade76512a0bb36b2e

Bug fixes:
- fixed tmRNA predictions that cross sequence origins: 90 (Thanks LuisFF)
- moved oriC/T/V product to Note in INSDC and compliant GFF3 outputs: https://github.com/oschwengers/bakta/commit/2f5cb1dae8da57c6d00dfbe66c0b3d48769b128e https://github.com/oschwengers/bakta/commit/716302e63b66c34a0e30bcea83c8818b6a0d2255 https://github.com/oschwengers/bakta/commit/5e1a0d831fa4d948aa459a5b8340f2a18afa2a6c
- fixed sequence description on Fasta import: https://github.com/oschwengers/bakta/commit/bfdf67f53ed0e3995a4cdaa8c227e12c9b122848
- fixed Fasta import log error: https://github.com/oschwengers/bakta/commit/52096727d857d44e98cfbb821094dbc8853b4a8b
- fixed EDAM out types in CWL file: https://github.com/oschwengers/bakta/commit/a1a0ad116f1a0e8133aa41877f3b67af599820a6

And of course all improvements and bug fixes from all v1.2.x patch releases.