v1.56

• Fix/Update: Improve creation of Prokka-like GFFs for Panaroo orthology inference. Panaroo expects gene-to-cds feature linking in the last column of GFFs. This is now added.
• Fix/Update: Add antiSMASH 8+ parsing support.
• Update Docker

Full Changelog: v1.55...v1.56

v1.55

• Major fix: Processing of pre-made full-genome GenBank files (e.g. from NCBI) - mainly affects the lsaBGC-Euk-Easy.py and lsaBGC-Ready.py programs. Previously, there was a possibility for partial processing of a genome resulting in incomplete genome files. This would specifically occur if a "translation" qualifier was missing for a CDS feature in some scaffold but always present in every CDS feature of the first scaffold in a multi-record GenBank file.
• Update remaining references of outdated names/links for SCG HMM database.

Full Changelog: v1.54...v1.55

v1.54

• update GToTree references to HMM models for Universal ribosomal proteins to use dashes instead of underscores.
• update handling of cases where genomes fail to be processed during BGC prediction or are dropped by GToTree when constructing a phylogeny in the lsaBGC-(Euk)-Easy workflows.

What's Changed

• update to v1.54 by @raufs in #31

Full Changelog: v1.53...v1.54

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