1.53

• update code for Panaroo based analysis to more comprehensively account for singleton gene, in particular those that might have been dropped.
• If using lsaBGC-EukEasy.py and resolved hierarchical orthogroups being determined by OrthoFinder - no special processing is performed as is the case for bacteria.
• remove SonicParanoid2 as dependency because of installation conflicts.
• Docker image updated to v1.53
• Added notice in README to consider switching to the new lsaBGC-Pan instead
  Full Changelog: v1.52...v1.53

1.52

• Removed faulty --taxon fungi argument in pre-generated antismash commands produced by lsaBGC-Easy.py.
• Docker images with & without sonicparanoid have been updated to latest version.

1.51

• Add missing indentation that caused issues with KO descriptions not being processed in util.py.

Full Changelog: v1.50...v1.51

v1.50

• Change-up handling of genes which were placed in coarse ortholog groups by OrthoFinder but are dropped off in the more resolved hierarchical ortholog groups. Instead of grouping the remaining genes into a bin identified by their original coarse (OG) names. Based on davidemms/OrthoFinder#288 , lsaBGC (lsaBGC-Ready specifically) will now parse the genes listed per genome in the Phylogenetically_Misplaced_Genes/ directory to and match them to their closest HOGs based on the relations with other genes reported in the Putative_Xenologs/ directory. The remaining "misplaced" genes will just be treated as singleton ortholog groups.
• Introduce Panaroo (🐀 ) as an option for determining ortholog groups - most appropriate for single bacterial species or lineages! 🎊
• Sonicparanoid removed from conda-based installation and now only available via Docker
• Update docker images to install older setuptools to avoid deprecation warning :/

What's Changed

• Update to v1.50 by @raufs in #29

Full Changelog: v1.40.0...v1.50

v1.40

• Update script for downloading annotation databases to account for changes in naming structure in the tar.gz directory with PGAP HMMs

v1.39

• Add code for changing antiSMASH BGC names to allow for non-unique scaffold names and enable proper parsing of BiG-SCAPE clustering downstream

What's Changed

• Update to v1.39 by @raufs in #25

Full Changelog: v1.38...v1.39

v1.38

Incorporation of SonicParanoid2 as an alternative method to OrthoFinder for delineation of ortholog groups.

What's Changed

• Update to v1.38: Incorporation of SonicParanoid2 by @raufs in #24

Full Changelog: v1.37.1...v1.38

v1.37.1

Important but minor corrections + updates:

• Correct default values for antiSMASH options in lsaBGC-Easy.py to not include the fungal flag.
• Allow BiG-SCAPE option to be provided (was previously set as a boolean argument in v1.37)
• Introduce explanation + code into wrapper for lsaBGC workflows to explain how to provide values for arguments with spaces, e.g. BiG-SCAPE options or antiSMASH options.

v1.37

• Update methods for determining BGC location in genomes.
• Introduce Docker + related code.
• Switch to MUSCLE super5 for default multiple sequence alignment of proteins per ortholog/homolog group (was previously MAGUS).

What's Changed

• Push v1.37 from develop branch to main by @raufs in #21

Full Changelog: 1.36...v1.37

v1.36

• update parsing of new PGAP HMM directory structure in setup_annotation_dbs.py
• improve checking to avoid having users continue to OrthoFinder with too many genomes.
• add features to lsaBGC-Easy/lsaBGC-Ready to be Docker compatible later.
• add more options for individual programs in wrapper workflows - including BiG-SCAPE and antiSMASH options in lsaBGC-Easy.