v1.2.0 - User provided proteins arrived ...

This is the second minor release (v1.2.0) introducing user provided proteins as well as many improvements.

Compatible database scheme version: 3 v3.0

New features:

• introduce --proteins accepting a user provided set of trusted protein sequences: 992d929 1541f10 691646d (Thanks to @Tonny-zhou)

Improvements:

• revise Dbxrefs for UniParc & UniRef: 02b5dc8
• revise truncated dnaA/repA genes on rotated replicon sequences: 0c4ad10 (Thanks to Jochen Blom)
• assign locus tags to gene features only: c1e1c05
• extract nt seqs for ncrna-regions: f77e308
• generate unique feature IDs used as ID in GFF3: df32038
• add products to oriC/oriV/oriT features: 2eabd93
• reduce numbers of similar to aa sequence inference qualifiers in INSDC outputs to 1: 16401da
• improve and fix CWL file: 6776ca7 1d18e77 5c80d15
• exrtact & store Pfam HMM hits on hypothetical proteins: 2ba985a

v1.1.1

This is the first v1.1 patch release (v1.1.1) providing a couple of improvements and minor bug fixes.

Compatible database scheme version: v3

Improvements:

• added a revision & refinement logic for gene symbols: 539137b
• added further CDS product revision rules: f8ec2aa 1fcca89 8915af7 626981b 321391b 0d93c2f #69 (Thanks @michoug)

Bug fixes:

• fixed AMRFinderDB issue in docker shell script: e825361
• fixed None values of CDS rbs_motif attributes: 0727b25
• skip CDS annotation if no CDS are predicted: 3787e01
• fix several CDS product revision rules

v1.1 - INSDC submission & annotation of MAGs: Hey! Ho! Let's go

This is the first minor release (v1.1) introducing several new features, many improvements and countless bug fixes.

Compatible database scheme version: 3 v3.0

New features:

• add new --compliant option for INSDC genome submissions: #69 (Thanks @michoug)
• introduce PSCCs (UniRef50) as a fallback if PSCs (UniRef90) are not detected, greatly improving the annotation of less represented species and metagenome-assembled genomes (MAGs): 84c808f
• export nucleotide sequences: #57 (Thanks @mcroxen)
• revise suspect CDS product names: f85970b

Improvements:

• various improvements and fixes in GFF3, GenBank and EMBL files to adhere to INSDC specs: #69
• improve internal DB download: bdd665a
• use Diamond version v2.0.11 and its --fast option: c82f4e2 19c95d8 (Thanks to @bbuchfink for bbuchfink/diamond#419)
• use stable CLI progress library alive-progress 0ac5625
• improve GFF3 output regarding GFF3 specs: 697121f
• store AMRFinderPlus DB within the Bakta DB directory: 04ff7b0 (Thanks to @LuisFF)
• redirect BAKTA-TMP directory to AMRFinderPlus to prevent stale files: 26f81fc
• detect & mark tmRNA on sequence edges: 782f640
• adhere to translation table in tmRNA prediction: 450d6b7

Bug fixes:

• fix var name in Docker shell script: e6bab09 (Thanks @joyn-sromero)
• fix inflated blastn thread numbers: e9073e1 (Thanks @LuisFF)
• fix location of features on sequence edges: 34873e7
• fix BLAST+ tool name in GFF3: efff065
  and many more ...

v1.0.4

This is the fourth v1.0 patch release (v1.0.4) fixing a couple of minor bugs and adding further minor improvements.

Compatible database scheme version: v2.0

Bug fixes:

• fixed an hmmsearch error if no CDS/sORF remain as hypotheticals: 9d4fc71 (Thanks Matthew Croxen)
• fixed a threadpool issue upon single core executions: 631fac6

Improvements:

• added GFF3 feature IDs to features w/o locus_tag: 08b8eae (Thanks @ZarulHanifah #54)
• add clipping of UniParc DB prefixes: c861af8 (Thanks Jochen Blom)

v1.0.3

This is the 3rd v1.0 patch release (v1.0.3).

Compatible database scheme version: v2.0

Bug fixes:

• activated the lookup of PSC if all CDS/sORF are identified as IPS which led to large amounts of false hypotheticals: 12df1af

Improvements:

• skip further analysis of spurious CDS/sORF: f22e114

v1.0.2

This is the second v1.0 patch release (v1.0.2) fixing a couple of minor bugs and adding further minor improvements.

Compatible database scheme version: v2.0

Bug fixes:

• fix a JSON NaN serialization issue: f8ff6b9 (Thanks @lukasjelonek )
• fix calculation of mol weight and isoelectric points for hypotheticals: b443e54
• fix duplicated annotation of ncRNA region features: 30df23c

Improvements:

• accept ambiguity NT codes in input fasta files: d4f615b
• add more tests: d8e67c0 (Thanks @Anna-Rehm )
• only write INSDC chromosome tags only on explicit names: efaf5cf
• write locus tag based GFF3 IDs to CRISPR and oriC/oriT/oriV: 04ed195 7a8242e (Thanks @ZarulHanifah #54)

v1.0.1

This is the first v1.0 patch release (v1.0.1) fixing some bugs & typos and add a couple of minor improvements.

Compatible database scheme version: v2.0

Bug fixes:

• fix calculation of GC & N50 stats: 2829a24 (Thanks Matthew Croxen)
• fix a typo in GenBank/EMBL output: 1595133 (Thanks @davised)

Improvements:

• download/update AMRFinderPlus db upon Bakta db download/update: 94ccc69
• add a short note to error msg if AMRFinderPlus db is not available: 750396f
• add more sORF unit tests: 685a3bc
• fix link to old db files: 140e348 (Thanks @davised)
• readme updates & improvements

v1.0 - In all beginnings dwells a magic force

This is the first official and stable v1.0 release introducing many new features and countless bug fixes.

Compatible database scheme version: 2 v2.0

New features and improvements over 0.5:

• expert annotation systems comprising AMRFinderPlus, BlastRules and VFDB
• support for EMBL flat files; INSDC-compliant and submission-ready, validated via ENA Webin-CLI
• db download from within Bakta: bakta_db --help
• parallelized sORF overlap filter significantly reduces wall clock runtimes
• replicon files can also be provided as CSV
• more integration tests added
• code reviews & optimizations
• updated readme and usage

as well as countless bug fixes.

v1.0-rc3

This is the 3rd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Bug fixes over rc2:

• several INSDC qualifier issues (1d0f6dc 1d0f6dc)
• INSDC tRNA anticodon and pseudo qualifier issues (ff668d5 fb03559)
• lacking python __init__ file (0560102)

Plus several minor bug fixes & improvements.

v1.0-rc2

This is the 2nd v1.0 release candidate introducing expert annotation systems incorporating AMRFinderPlus, BlastRules and VFDB.

Improvements over rc1:

• added parameter argument checks
• added more tests
• updated usage and readme

Bug fixes:

• fixed name of main entry module