v1.5.3

• Update processing of miniprot mapping results done in prepTG, including: switching to the most updated miniprot version (v0.13), using PAF cigar string alone to redetermine CDS coordinates, changing the field qualifiers for CDS features in created GenBank files, and adding the -I argument when running miniprot to have it auto set the max allowed intron size.
• Update fai's GenBank creation for extracted gene clusters to avoid including partial CDS features when multiple-exons are present and the boundary for the gene cluster falls in an intronic region.

What's Changed

• Update util.py by @raufs in #84

Full Changelog: v1.5.2...v1.5.3

v1.5.2

• Correct inclusion of all hits when using --domain-mode in zol, now restricted to only "trusted" domain hits.
• Add data dictionary tables to first sheets of fai and zol results instead of just having a link to the wiki.
• Add progress bars to multiprocessing steps in prepTG, fai, and zol.
• Use rich-argparse to have color coding for help functions of all major programs.
• Correct issues with providing GenBank files as input for prepTG to create a target genomes database.

What's Changed

• Update zol.py by @raufs in #83

Full Changelog: v1.5.1...v1.5.2

v1.5.1

• Slight updates to cgcg :
  • Correct for the lack of "consensus directionality" for ortholog groups represented in figures which can lead to misinterpretation of gene order.
  • Add more options to control graph, including an option to show the major ortholog group path observed across gene cluster instances.
• Some changes to docker image building files.

What's Changed

• Update README.md by @raufs in #80
• Update README.md by @raufs in #81
• Update meta.yaml by @raufs in #82

Full Changelog: v1.5.0...v1.5.1

v1.5.0

Major updates:

• Introduce cgcg for interactive network visualization of homologous instances of gene clusters.
• Introduce domain-mode in zol. Uses pyhmmer to identify Pfam domains in CDS features in gene clusters to chop the CDS features up by domains and perform domain-centric analyses instead of protein-centric analyses. Identifies domain-ortholog groups (DOGs 🐶 ) Useful for dealing with gene clusters featuring ginormous genes, such as PKSs or NPRSs.
• Introduce zol-scape a simple wrapper of BiG-SCAPE to run zol on each GCF it identified to complement visual views produced by CORASON.
• Upgrade project organization by addition of pyproject.toml , adjust setup.py, and get rid of Rscript references. Rscripts are now created de novo within result directories allowing users to customize them as needed.

Minor updates:

• correct extraction of phage instances which are annotated as entire contigs/scaffolds by geNomad in atpoc.
• minimal-mode in the database downloading script now includes Pfam HMMs in addition to PGAP HMMs.

What's Changed

• Update to v1.5.0 by @raufs in #78
• Update CITATION.cff by @raufs in #79

Full Changelog: v1.4.12...v1.5.0

v1.4.12

• add option for downloading minimal databases for lsaBGC-Pan

v1.4.11

• correct issue with cpus argument for pyhmmer being accidentally renamed to threads in the switch of terminology from cpus to threads for zol code made in v1.4.10
• add option to skip annotations in zol, --skip-annotations
• add shebang in annotateProtaSeqs.py to make it executable.

Full Changelog: v1.4.10...v1.4.11

v1.4.10

minor updates

• update and further polish arguments (e.g. underscores to dashs).
• add --small-genomes preset flag for skani based dereplication in zol.
• (for bioconda) planning on adding constraints on versions for some dependencies (e.g. muscle>=5.0)
  Full Changelog: v1.4.9...v1.4.10

v1.4.9

• Add small script for standalone annotation using zol's standard annotation approach for consensus sequences of ortholog groups called annotateProtSeqs.py.

What's Changed

• Update README.md by @raufs in #73
• Update annotateProtSeqs.py by @raufs in #74

Full Changelog: v1.4.8...v1.4.9

v1.4.8

• re-configure where multiprocessing.set_start_method() is set in fai and add catches for possible issues to work as intended on newer Macs.
• add cgc command to tests

What's Changed

• Update setup.py by @raufs in #72

Full Changelog: v1.4.7...v1.4.8

v1.4.7

• Update usage of pomegrenate for HMM mode in fai for finding gene clusters to account for API changes.
• This is largely to update versions for some dependencies (mainly biopython and pomegrenate) in bioconda to assist in the transition to newer python versions.