[Bioperl-l] Is it possible to do contig alignments?
florent.angly at gmail.com
Fri Aug 24 13:58:13 EDT 2007
Chris Fields wrote:
> A similar question has been previously asked on the same subject:
> Jason's suggestion was to have a Bio::Assembly::Contig method
> get_aln() which produces a Bio::SimpleAlign object containing
> appropriately padded seqs compatible for AlignIO output. However, the
> method was never implemented.
> Personally, the way I would try going about this would be to implement
> the Contig::get_aln() method, padding with bioperl-compliant alignment
> gap symbols (currently -.*?=~), so if anyone wanted they could write
> to any AlignIO-implemented format (MSF, Clustal, etc). In your
> Bio::Assembly::IO::simpleout module implement write_assembly() and use
> the Contig::get_aln() method where needed to grab the SimpleAlign,
> then simply substitute gap symbols with spaces when writing contig
> In general, any new code is attached to a bugzilla report as an
> enhancement request:
> One of the devs will work on getting the code incorporated into
> bioperl. Make sure the code is documented
> (http://www.bioperl.org/wiki/Advanced_BioPerl), and attach appropriate
> tests (http://www.bioperl.org/wiki/HOWTO:Writing_BioPerl_Tests) and
> test data.
Thanks Chris for the pointers, I will be looking into these things.
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