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Project description
CoRecomb: create a XMFA file from Panaroo core gene alignments to detect recombination in core-genome using ClonalFrameML
Installation
pip install corecomb
Quick start
If you are in Panaroo output directory, just run:
corerecomb
Get help
$ corecomb --help
Usage: corecomb [OPTIONS]
Create XMFA file from ClonalFrameML input from Panaroo core-genome gene alignments
╭─ Options ───────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╮
│ --gene_al_dir TEXT Path to directory containing core-genome gene alignments [default: core_gene_alignments] │
│ --pan_fa TEXT Path to Panaroo pan_genome_reference.fa [default: pan_genome_reference.fa] │
│ --extension TEXT File extension of core-genome gene alignments [default: fas] │
│ --outfile TEXT Path to output XMFA file [default: corecomb.xmfa] │
│ --help Show this message and exit. │
╰─────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────╯
Test it for yourself
poetry run pytest -vv
Test data can be found here tests/data
corecomb \
--gene_al_dir tests/data/aligned_gene_sequences_raw \
--pan_fa tests/data/pan_genome_reference.fa \
--extension fas \
--outfile corecomb.xmfa
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