v1.10.1

This is the first v1.10 patch release (v1.10.1).

Improvements

• Improved handling of draft genome in circular plots: 0118983
• Added N90 to genome statistics: 7abfa9a

Fixes

• Fixed changed Micromamba parameter in Dockerfile: #342 #345 (Thanks @pamelacamejom / @mjfos2r)
• Fixed INSDC note qualifiers: #346 (Thanks @Dx-wmc)

v1.10 - Novel in & novel out

This is the tenth minor release (v1.10) introducing user-provided HMMs, output file recovery, feature inference scores, and various improvements.

Compatible database scheme version: 5

Important

Since v1.10.0, Bakta requires Python >=3.9, uses pyCirclize instead of Circos, and discarded support of DeepSig!

An important decision had to be made for this release regarding supported Python versions, external dependencies and features impacted by this. Both Circos and DeepSig seem to be out of support for a long time. Hence, Circos was replaced by pyCirclize, a pure-Python actively-maintained library, enabling a couple of new features. As a result, Bakta's Python dependency had to be bumped to >=3.9, thus unfortunately loosing compatibility with DeepSig. Dropping an existing feature feels odd and wrong, but as a developer, sticking to unmaintained external software for too long constantly increases your daily pain level and slows down the project as a whole. This hasn't been an easy decision, but a necessary. So, If you depend on the detection of signaling peptides, please keep using Bakta <=v1.9.4.

New features

• Accept user-provided trusted HMMs via --hmms: #309 #327 (Thanks @StefDiV)
• Recover output files based on Bakta's comprehensive JSON output via bakta_io: #304 #339 (Thanks @cpauvert)
• Write annotation inference metrics to new *.inference.tsv file: #314 #331 (Thanks @jvera888 / @gbouras13)
• Deactivate feature overlap filters via --skip-filter : #295 (Thanks @Daniel-Tichy)

Improvements

• Support translation table 25: #323 (Thanks @ndombrowski)
• Export CRISPR and tRNA nucleotide sequences: #336 (Thanks @YoungerRen)
• Replacement of Circos by pyCirclize: #344 (Thanks @acarafat / @alexweisberg)
• Introduce --label, --size and --dpi parameters in bakta_plot to customize plots: #344
• Add fixes for common submission errors: #330 (Thanks @kevinmyers)
• Improve INSDC compliance: 30b3928 8ba8a14
• Reduce the locus tag offset from 5 to 1 and allow specifications via --locus-tag-increment: #279 (Thanks @1996xjm)
• Revise internal/external designation of truncated features and (real) pseudogenes: #333
• Print msg if IPS and pseudogene detection is skipped using the db light version: #320 (Thanks @flashton2003)
• Review internal main data structure: #338

Fixes

• Fix import of user-provided CDS spanning sequence edges: #324 #332 (Thanks @aekazakov)
• Fix translated protein sequences for CDS truncated at both sides: #340 (Thanks @tpillone)
• Fix wrong truncation label: #341
• Fix import of user-provided regions in combination with a metadata replicon table: #326

Full Changelog: v1.9.4...v1.10.0

v1.9.4

This is the fourth v1.9 patch release (v1.9.4).

Fixes

• Fixed CDS gene translation in meta mode: #301 (Thanks @ohickl)
• Fixed the CRISPR parser for short (<10 nt) spacer sequences: #299 #302 (Thanks @ohickl)
• Fixed Pyrodigal and Pyhmmer version detection: #294 (Thanks @EricDeveaud)

Improvements

• Skip certain genes in user-provided regions: #288 #303 (Thanks @Dx-wmc)

v1.9.3

This is the third v1.9 patch release (v1.9.3).

Fixes

• fixed a regex in the CRISPR parser skipping spacers in some special cases: c747803 #265 (Thanks @ZarulHanifah)
• fixed wrong Piler-CR CRISPR array stop position omitting the last spacer: #276
• tmp. pinned Diamond version to v2.1.8 due to an upstream bug: 0dd84fb

Improvements

• added parent ID to CRISPR repeat/spacer features in GFF3 outputs: ae71c09

v1.9.2

This is the second v1.9 patch release (v1.9.2).

Fixes

• Changed tRNA pseudogene type to unknown in INSDC compliant mode: bb8366a
• Updated DB build scripts for v5.1: #270
• Allow uneven number of CRISPR spacers/repeats: #265 #267 7c1a7e8 (Thanks @ZarulHanifah, @marade)
• Fixed wrong complete sequence inference for some cases: 231788b 24a43b9
• Fixed minor issues with DB downloads/updates: 4d609de 1a0413c ff836d1

v1.9.1

This is the first v1.9 patch release (v1.9.1).

Fixes

• Fixed a Python KeyError when both --regions and --keep-contig-headers are used: d3d7a98 (Thanks @thorellk)
• Fixed a bzip2 error in the Docker build process: 73ac39d (Thanks @lukasjelonek)

v1.9 - Here's my region of interest

This is the ninth minor release (v1.9) introducing user-provided feature regions and various minor improvements.

Compatible database scheme version: 5

New features

• Support a priori user-provided feature regions via --regions either in Genbank or GFF3 format (currently, only CDS features are supported). CDS coordinates are imported, supersede de novo predicted CDS, and are subject to the regular internal annotation workflow. To provide functional annotation, as well use --proteins: #216 #245 #247 #250 #259 (Thanks @marade @PengfanZhang @simone-pignotti @thorellk)

Improvements

• Extract & export CRISPR spacer & repeat sequences: #171 #249 (Thanks @alexweisberg)
• Add support for Pyrodigal v3: #240 #244 (Thanks @jsgounot)
• Replace HMMER with PyHMMER: #219 (Thanks @jhahnfeld)
• Re-activate parallel pyrodigal gene prediction: #252 (Thanks @althonos)
• Introduce auxiliary scripts: #246 #251 (Thanks @AhmedElsherbini)
• Add Podman wrapper script: bd50faa
• Update dependencies to latest versions: 3260441 33c02f9 a1d2ffe b265672 1a2c48e

Fixes

• Fix PyPI CD: #231
• Add missing --force parameter to Docker wrapper script: f39434e
• Fix wrong runtime report: #243

Full Changelog: v1.8.2...v1.9.0

v1.8.2

This is the second v1.8 patch release (v1.8.2).

Improvements:

• Replacd HMMER by PyHMMER: 3415e89 (Thanks @jhahnfeld)
• Refactored & improved CI scripts
• Refactored the code
• Tweaked code to expand required BioPython versions: 6a88c4b (Thanks @alexweisberg)
• Deactivated --force parameter for the current working directory`: a039bec
• Added Pyrodigal to dependency checks: 17bcfc9

Bug Fixes:

• Fixed and improved the CWL wrapper: #221 #229 #230 (Thanks @bartns & @jjkoehorst)

v1.8.1

This is the first v1.8 patch release (v1.8.1) catching up an overlooked PR.

Improvements:

• Added all valid expert system hits to the final dbxrefs and JSON results: #198 #199 (Thanks @davidtong28)

Important:
#199 introduced a breaking change in the JSON data structure of the feature->expert section. expert was changed from a dictionary (expert system -> hit) to a flat list of expert hits now having a new type field.

v1.8 - May the --force (parameter) be with you

This is the eighth minor release (v1.8) introducing a new output option and various minor improvements.

Compatible database scheme version: 5

Improvements:

• Introduced a new --force option explicitly allowing to overwrite existing data: #200 (Thanks @Dx-wmc)
• Increased sensitivity of protein sequence expert system: #197 (Thanks @davidtong28)
• Improved compatibility of FNA output with NCBI Bankit Submission: #201 (Thanks @menickname)
• Improved --plasmid parameter functionality: #201 426bfd3
• Introduced output of bakta_proteins full annotation results as JSON: #204 (Thanks @Rridley7)
• Refactored QC and description of imported genome sequences: af835b4

Fixes:

• Fixed rare occasions of wrong 5' / 3' ("prime") characters in product descriptions: #215 (Thanks @axbazin)