[Bioperl-l] Is it possible to do contig alignments?

Florent Angly florent.angly at gmail.com
Fri Aug 24 17:58:13 UTC 2007

Chris Fields wrote:
> A similar question has been previously asked on the same subject:
> http://thread.gmane.org/gmane.comp.lang.perl.bio.general/2827/focus=2869
> 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 
> output.
> In general, any new code is attached to a bugzilla report as an 
> enhancement request:
> http://bugzilla.open-bio.org/
> 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.
> chris
Thanks Chris for the pointers, I will be looking into these things.

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