lsabgc-pan - v1.1.7

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

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.6...v1.1.7

- Python
Published by raufs 10 months ago

lsabgc-pan - 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 https://github.com/Kalan-Lab/lsaBGC-Pan/issues/14

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.5...v1.1.6

- Python
Published by raufs 10 months ago

lsabgc-pan - v1.1.5

• Slight update to properly parse antiSMASH >v8 GBKs.

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.4...v1.1.5

- Python
Published by raufs 11 months ago

lsabgc-pan - 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 https://github.com/Kalan-Lab/lsaBGC-Pan/pull/13

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.3...v1.1.4

- Python
Published by raufs 11 months ago

lsabgc-pan - v1.1.3

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

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.2...v1.1.3

- Python
Published by raufs about 1 year ago

lsabgc-pan - 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 https://github.com/Kalan-Lab/lsaBGC-Pan/issues/11

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.1...v1.1.2

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.1.0...v1.1.1

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.9...v1.1.0

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.8...v1.0.9

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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 https://github.com/Kalan-Lab/lsaBGC-Pan/issues/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: https://github.com/Kalan-Lab/lsaBGC-Pan/issues/5

Updates to lsaBGC-Sociate

• Corrected issue related to blank "notes" fields in pyseer - related to Issue/Request https://github.com/Kalan-Lab/lsaBGC-Pan/issues/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 https://github.com/Kalan-Lab/lsaBGC-Pan/issues/7

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.6...v1.0.7

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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.

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.4...v1.0.5

- Python
Published by raufs almost 2 years ago

lsabgc-pan - 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: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.3...v1.0.4

- Python
Published by raufs almost 2 years ago

lsabgc-pan - v1.0.3

• correct title in CITATION.cff

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/compare/v1.0.2...v1.0.3

- Python
Published by raufs almost 2 years ago

lsabgc-pan - v1.0.2

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

- Python
Published by raufs almost 2 years ago

lsabgc-pan - v1.0.0

Initial release

Full Changelog: https://github.com/Kalan-Lab/lsaBGC-Pan/commits/v1.0.0

- Python
Published by raufs almost 2 years ago