Option to ignore shared substitutions - Githubissues

lenaschimmel / sc2rf

SARS-Cov-2 Recombinant Finder for fasta sequences

MIT License

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Option to ignore shared substitutions #30

Open ktmeaton opened 2 years ago

ktmeaton commented 2 years ago

I've been experimenting with a flag --ignore-shared that ignores positions that are shared (have the exact same nucleotide) across all parents/examples.
I like this option because it makes the breakpoints visually clearer, as there's a direct color change (red -> green) rather than having the intermediate shared positions (red -> white -> green)
For testing, a nextclade fasta alignment of XM-like recombinants (public on genbank): XM.txt

Do you think this is scientifically sound for reporting? And if so,
Would you be interested in a PR if I tidy up the code?

Default Output:

python3 sc2rf.py XM.fasta --ansi --unique 1

Proposed Option:

python3 sc2rf.py XM.fasta --ansi --unique 1 --ignore-shared