v1.5.8

Minor Updates

• When running in single-query mode in fai, fix construction of the final spreadsheet.
• Add shebang for script executables which were missing it.

What's Changed

• 1.5.8 by @raufs in #92

Full Changelog: v1.5.7...v1.5.8

v1.5.7

Minor updates

• Improve legibility/logic of code for domain coordinate determination - leads to difference in coordinates but not with consensus order/direction and gene-order inference on some test cases relative to the previous version.
• Add sorting to cases where for a functional database there are multiple tied best matching targets to the consensus sequence of an ortholog group to aid deterministic behavior for generation of zol consolidated reports.

Full Changelog: v1.5.6...v1.5.7

v1.5.6

• Corrected coordinates and consensus order/direction inference for zol "domain mode".

Minor improvements / fixes

• Make --select-fai-params-mode more robust to cases where input gene cluster instances only have 1 ortholog group in common and corrected outputing of FASTA output for near-core representative proteins (#88).
• Added flag in zol to avoid replacing start proteins with M if they are instead L or V based on direct translation if eukaryotic analysis is being performed: --eukaryotic-gene-cluster (#89)
• Correct generateSyntenicVisual.py usage with new setup which generates R scripts (#90).
• Updated cgcg to also work with results from "domain mode".
• Added options to control inflation parameter for MCL and to perform simple single-linkage clustering for ortholog group delineation (#91).
• Improved argument descriptions for prepTG, fai, zol
• Added overwrite / remove directory clearing for select fai/zol steps.
• Re-introduced edge weights in cgcg and added an option for minimum edge weight to show.
• Now report whether Beta-RD calculation is requested in the zol parameters file and also whether mge-annotation was used in prepTG
• Fixed salt being broken in update to v1.5.0
• Now right-strip "*" characters (stop codons) from sequences in prepTG databases
• Corrected automatic coloring in "instances" sheet of fai spreadsheet.

What's Changed

• update to v1.5.6 by @raufs in #87

Full Changelog: v1.5.5...v1.5.6

v1.5.5

Minor updates:

• Usually, environment variable OMP_NUM_THREADS is set to 1 on most systems, but, in case this is not the case, the environment variable is now set to 1 at the beginning of major executable programs.
• Add sorting when assigning locus tags to genomes in prepTG to make multiple runs more deterministic.

What's Changed

• Update CITATION.cff by @raufs in #85

Full Changelog: v1.5.4...v1.5.5

v1.5.4

• Fix possibility for zol to get stuck inside a while loop for determining the major/consensus path. Please avoid using v1.5.1 to v1.5.3!

Full Changelog: v1.5.3...v1.5.4

v1.5.3

Caution

Please do not use! This version features the possibility for zol to get stuck in a while loop and write large files.

• Update processing of miniprot mapping results done in prepTG, including: switching to the most updated miniprot version (v0.13), using PAF cigar string alone to redetermine CDS coordinates, changing the field qualifiers for CDS features in created GenBank files, and adding the -I argument when running miniprot to have it auto set the max allowed intron size.
• Update fai's GenBank creation for extracted gene clusters to avoid including partial CDS features when multiple-exons are present and the boundary for the gene cluster falls in an intronic region.

What's Changed

• Update util.py by @raufs in #84

Full Changelog: v1.5.2...v1.5.3

v1.5.2

Caution

Please do not use! This version features the possibility for zol to get stuck in a while loop and write large files.

• Correct inclusion of all hits when using --domain-mode in zol, now restricted to only "trusted" domain hits.
• Add data dictionary tables to first sheets of fai and zol results instead of just having a link to the wiki.
• Add progress bars to multiprocessing steps in prepTG, fai, and zol.
• Use rich-argparse to have color coding for help functions of all major programs.
• Correct issues with providing GenBank files as input for prepTG to create a target genomes database.

What's Changed

• Update zol.py by @raufs in #83

Full Changelog: v1.5.1...v1.5.2

v1.5.1

Caution

Please do not use! This version features the possibility for zol to get stuck in a while loop and write large files.

• Slight updates to cgcg :
  • Correct for the lack of "consensus directionality" for ortholog groups represented in figures which can lead to misinterpretation of gene order.
  • Add more options to control graph, including an option to show the major ortholog group path observed across gene cluster instances.
• Some changes to docker image building files.

What's Changed

• Update README.md by @raufs in #80
• Update README.md by @raufs in #81
• Update meta.yaml by @raufs in #82

Full Changelog: v1.5.0...v1.5.1

v1.5.0

Major updates:

• Introduce cgcg for interactive network visualization of homologous instances of gene clusters.
• Introduce domain-mode in zol. Uses pyhmmer to identify Pfam domains in CDS features in gene clusters to chop the CDS features up by domains and perform domain-centric analyses instead of protein-centric analyses. Identifies domain-ortholog groups (DOGs 🐶 ) Useful for dealing with gene clusters featuring ginormous genes, such as PKSs or NPRSs.
• Introduce zol-scape a simple wrapper of BiG-SCAPE to run zol on each GCF it identified to complement visual views produced by CORASON.
• Upgrade project organization by addition of pyproject.toml , adjust setup.py, and get rid of Rscript references. Rscripts are now created de novo within result directories allowing users to customize them as needed.

Minor updates:

• correct extraction of phage instances which are annotated as entire contigs/scaffolds by geNomad in atpoc.
• minimal-mode in the database downloading script now includes Pfam HMMs in addition to PGAP HMMs.

What's Changed

• Update to v1.5.0 by @raufs in #78
• Update CITATION.cff by @raufs in #79

Full Changelog: v1.4.12...v1.5.0

v1.4.12

• add option for downloading minimal databases for lsaBGC-Pan