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

v1.1.0

• Set and reset OMP_NUM_THREADS env variable to 1 around steps where R is parallelized to allow threads to still be used for MUSCLE alignment and other operations.

Full Changelog: v1.0.9...v1.1.0

v1.0.9

Note, release v1.0.8 deleted because intended changes pertaining to removal of -strict in lsaBGC-Reconcile were not committed - however it is still tracked via Zenodo if of interest.

• Add catches for rare cases when trimal trimmed alignment produces a blank output.
• Remove -strict for trimal usage in lsaBGC-Reconcile to create orthogroup trees (note, option is still kept for construction of species tree in phylogenate).
• Set OMP_NUM_THREADS env variable in lsaBGC-Pan to prevent Rscript executions for plotting from using > 1 thread.

Full Changelog: v1.0.8...v1.0.9

v1.0.7

General workflow changes:

• Split lsaBGC-Reconcile and lsaBGC-Sociate into separate steps.
• Introduced running of cgc in step 7 when zol is run - related to Issue/Request #8
• New options for downstream running of lsaBGC-Sociate and lsaBGC-Reconcile
• Timeout introduced for creating protein alignments with MUSCLE in lsaBGC-Reconcile and lsaBGC-Sociate. Previously this can lead to abnormally large orthogroups just straggling the pipeline/workflow. Default timeout now set to 30 minutes.
• Corrected bug introduced in lsaBGC-Reconcile in v1.0.6 - as mentioned in Issue: #5

Updates to lsaBGC-Sociate

• Corrected issue related to blank "notes" fields in pyseer - related to Issue/Request #6
• KEY: More conservative filtering of lsaBGC-Sociate results to disregard hits with something in the "notes" field - e.g. if firth regression used in place of lmm.
• New phylo-heatmap showing associated features with focal GCFs alongside the species tree lsaBGC-Sociate: related to Issue/Request #7

Full Changelog: v1.0.6...v1.0.7

v1.0.6

• Improve input argument description and flexibility for providing raw genomes in FASTA format.
• Switch from multiprocessing to concurrent.futures to ease throttling for large jobs
• Improve runtime by computing orthogroup conservation among complete instances of a GCF using a function rather than employing a full zol run.

v1.0.5

• Correct four column simple BGC listing creation error introduced in v1.0.4 that affected lsaBGC-MIBiGMapper, lsaBGC-See, and lsaBGC-ComprehenSeeIve analyses.
• Add download & parsing of MIBiG json for annotation of compounds BGC IDs correspond to in the consolidated spreadsheet

Full Changelog: v1.0.4...v1.0.5

v1.0.4

• Add option to lsaBGC-Cluster and lsaBGC-Pan to allow for leniency in clustering BGCs near contig edges to reduce the number of singleton GCFs
• Improve readability of the help function for lsaBGC-Pan
• Expand descriptions of products for multi-type BGCs in the "BGC Overview" spreadsheet

Full Changelog: v1.0.3...v1.0.4

v1.0.3

• correct title in CITATION.cff

Full Changelog: v1.0.2...v1.0.3

v1.0.2

• Improvements to help function clarity / correctness.
• Add links in messages to documentation on wiki.
• Will be added to Zenodo for tracking.