lsabgc - 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 https://github.com/Kalan-Lab/lsaBGC/pull/31

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/v1.53...v1.54

- Python
Published by raufs 11 months ago

lsabgc - 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: https://github.com/Kalan-Lab/lsaBGC/compare/v1.52...v1.53

- Python
Published by raufs over 1 year ago

lsabgc - 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.

- Python
Published by raufs about 2 years ago

lsabgc - 1.51

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

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/v1.50...v1.51

- Python
Published by raufs about 2 years ago

lsabgc - 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 https://github.com/davidemms/OrthoFinder/issues/288 , lsaBGC (lsaBGC-Ready specifically) will now parse the genes listed per genome in the PhylogeneticallyMisplacedGenes/ 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 https://github.com/Kalan-Lab/lsaBGC/pull/29

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/v1.40.0...v1.50

- Python
Published by raufs over 2 years ago

lsabgc - v1.40

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

- Python
Published by raufs over 2 years ago

lsabgc - 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 https://github.com/Kalan-Lab/lsaBGC/pull/25

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/v1.38...v1.39

- Python
Published by raufs over 2 years ago

lsabgc - 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 https://github.com/Kalan-Lab/lsaBGC/pull/24

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/v1.37.1...v1.38

- Python
Published by raufs over 2 years ago

lsabgc - 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.

- Python
Published by raufs almost 3 years ago

lsabgc - 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 https://github.com/Kalan-Lab/lsaBGC/pull/21

Full Changelog: https://github.com/Kalan-Lab/lsaBGC/compare/1.36...v1.37

- Python
Published by raufs almost 3 years ago

lsabgc - v1.36

• update parsing of new PGAP HMM directory structure in setupannotationdbs.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.

- Python
Published by raufs almost 3 years ago

lsabgc - v1.35

Make default to not run lsaBGC-AutoExpansion in lsaBGC-Easy, add new program to make assessment of lsaBGC-AutoExpansion results in lsaBGC-Easy simplified/streamlined, and change handling of researching of primary genomes (those used for OrthoFinder analysis) with AutoExpansion.

- Python
Published by raufs almost 3 years ago

lsabgc - v1.34

New programs: Introduce lsaBGC-MIBiGMapper, lsaBGC-Euk-Easy, and visualize_BGC-ome

Updated README + documentation.

- Python
Published by raufs almost 3 years ago

lsabgc - v1.33

• Added support for DeepBGC and GECCO annotation parsing into GSeeF
• Incorporated GSeeF into the end of the lsaBGC-Easy workflow
• Better handling of input genomes with similarly named scaffolds in lsaBGC-Ready/Easy

- Python
Published by raufs almost 3 years ago

lsabgc - v1.32

• Add option to change the length of window of ambiguity in lsaBGC-DiscoVary.
• Use bitscores instead of E-values for assigning genes to homolog groups in lsaBGC-Expansion. E-values are still used for specifying cutoffs and the final polishing to check if expansion of BGC segments are possible.
• Fix recently introduced bug to allow lsaBGC-PopGene to be run without expected genome-wide differences provided.

- Python
Published by raufs about 3 years ago

lsabgc - 1.31

Much improved logging for lsaBGC-Easy, more robust GSeeF, & updated codon-usage-based BGC assimilation assessment program.

- Python
Published by raufs about 3 years ago

lsabgc -

Introduce GSeeF, update to using HOGs instead of OGs with OrthoFinder, etc.

- Python
Published by raufs over 3 years ago

lsabgc - 1.2

Update pop-gene report to more easily report to users which homolog groups are not single copy in the context of a GCF.

- Python
Published by raufs over 3 years ago

lsabgc - v1.1

Introduction of lsaBGC-Easy.py

- Python
Published by raufs over 3 years ago

lsabgc - Initial Release

Version 1 - Initial release of lsaBGC

- Python
Published by raufs almost 4 years ago