clinker v0.0.31

Full Changelog: v0.0.30...v0.0.31

• Fix bug in logger statement when shifting origin
• Check for undefined sequence when parsing input files (requires BioPython >=1.80)

clinker v0.0.30

What's Changed

• ✨ feat: enhancement #113 by @Aurorabili in #114

New Contributors

• @Aurorabili made their first contribution in #114

Full Changelog: v0.0.29...v0.0.30

clinker v0.0.29

Full Changelog: v0.0.28...v0.0.29

• Add uppercase ID to list of gene identifiers (fixes #110)

clinker v0.0.28

• Added colour map argument when specifying groups

clinker v0.0.27

• Explicitly check for BioPython version when splitting Alignment/PairwiseAlignment objects instead of try/except

clinker v0.0.26

• Fixed an issue with parsing pairwise alignments after changes to default printed format in BioPython v1.80 (biopython/biopython#4183). Should now work fine pre/post v1.80. (#91)

clinker v0.0.25

• Fix crash when no CDS features are found parsing GFF records (#10)

clinker v0.0.24

• Don't open web browser after creating static HTML when file name is provided (#88)

clinker v0.0.23

• Added -gf/--gene_functions argument for grouping genes by shared function/category, instead of just sequence similarity.

Given a 2-column CSV resembling:

GENE_001,Cytochrome P450 
GENE_002,Cytochrome P450 
GENE_003,Methyltransferase
GENE_004,Methyltransferase

Two groups are generated, Cytochrome P450 (GENE_001 and 002), and Methyltransferase (GENE_003, GENE_004).

• Updated clustermap.js. Gene groups now have tooltips when the corresponding label in the legend is right-clicked, and can now be easily merged to combine groups that share some function/category that did not group together by similarity alone

clinker v0.0.22

• Bumped BioPython minimum version to >=1.78 for select method in substitution matrices (biopython/biopython#3205)
• Added -mo, --matrix_out argument for saving cluster alignment distance matrix to a file