zol

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 https://github.com/Kalan-Lab/zol/pull/78
• Update CITATION.cff by @raufs in https://github.com/Kalan-Lab/zol/pull/79

Full Changelog: https://github.com/Kalan-Lab/zol/compare/v1.4.12...v1.5.0