[BioRuby] Clustal ALN writer
Pjotr Prins
pjotr.public14 at thebird.nl
Tue Jan 5 12:39:02 UTC 2010
I propose to write an ALN output writer. ALN files show aligned
sequences with additional lines of information (like a match line). I
want to use it to output PAML positive selection sites. This is
the idea:
SEQ1 alignment 1...
SEQ2 alignment 2...
...*.:*....*** (match line)
...*....*..... (pos. sel. line)
Do we want such ALN output (I think it is allowed), and can we allow
for the additional output. I have a proposed interface here:
http://github.com/pjotrp/bioruby/commit/7f320781039b56aee991ab72404655fae210e2cb
I notice ClustalW.to_fasta has been obsoleted. But we don't have
to_aln yet, and we need to allow adding match_lines and other
information.
Pj.
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