corecomb 0.2

No project description provided

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