v1.1.10

• Fix: Reporting of coordinates for antiSMASH BGCs in the "BGC Overview" sheet of the final consolidated spreadsheet (were previously off by 1).
• Add: New note in lsaBGC-Pan's help function that clarifies how names of antiSMASH results folders will be used as sample names (controlled by antismash's --output-dir argument) instead of the full-genome GenBank file names (controlled by antismash's --output-basename option).

Full Changelog: v1.1.9...v1.1.10

v1.1.9

• Add: Suggestions on what to do if it appears you have OrthoFinder / Panaroo not installed or properly setup.
• Update: Switch from invoking FastTree 2 as FastTree instead of fasttree to avoid issues on certain platforms.

Full Changelog: v1.1.8...v1.1.9

v1.1.8

• Update/Fix: 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.
• Minor Update/Fix: Improve logging in phylogenate.
• Update/Fix: Accounts for new changes to zol reports and requires version > 1.6.9.
• Fix: Consolidation of zol reports across GCFs when the -zhq option is used.

Full Changelog: v1.1.7...v1.1.8

v1.1.7

Minor changes to switch to curl from axel to allow for easier installation on macOS via Bioconda.

Full Changelog: v1.1.6...v1.1.7

v1.1.6

• Fix issues with using --keep-locus-tags / -k which might have led to failed jobs. This option is now noted as experimental as there might still be further issues in handling / expectations.
• Add progress bars for parallelized steps and some more safety catches.
• Speed up processing of finding antiSMASH BGC locations in genomes using indexing - should speed up fungal analyses significantly.
• Solve issue with phylogenate referencing iqtree found in #14

Full Changelog: v1.1.5...v1.1.6

v1.1.5

• Slight update to properly parse antiSMASH >v8 GBKs.

Full Changelog: v1.1.4...v1.1.5

v1.1.4

• Update to account for updated report in zol v1.5.16+
• Update to avoid use of deprecated pkg_resources API
• Correct initialization of variable issue in lsaBGC-Sociate

What's Changed

• Update to v1.1.4 by @raufs in #13

Full Changelog: v1.1.3...v1.1.4

v1.1.3

• Update to handle using newer versions of zol.
• Update to handle using MIBiG v4.0 from v3.1.

Full Changelog: v1.1.2...v1.1.3

v1.1.2

Minor changes:

• clean up and correct descriptions for some arguments in some scripts/ programs.
• improve code documentation by adding function details in the util.py module and BGC.py, GCF.py, and Pan.py classes - related to issue/improvement-ticket #11

Full Changelog: v1.1.1...v1.1.2

v1.1.1

Changes to lsaBGC-Sociate

• Make lsaBGC-Sociate more conservative by applying multiple testing correction using Bonferroni adjustment of alpha account for all tests cumulatively; no longer applied individually per focal GCF.
• Add columns in lsaBGC-Sociate showing percentage of samples with the focal GCF which have the associated/dissociated trait (p) and also the percentage of samples without the focal GCF which have the associated/dissociated trait (q).
• Change coloring in plots to reflect whether p > q (can be regarded as associated with focal GCF) or p < q (can be regarded as dissociated with focal GCF) instead of whether beta is positive or negative.

Full Changelog: v1.1.0...v1.1.1