[Biopython-dev] [Bug 2560] New: Adding BLAST support to Bio.AlignIO

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2560

           Summary: Adding BLAST support to Bio.AlignIO
           Product: Biopython
           Version: Not Applicable
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: enhancement
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: biopython-bugzilla at maubp.freeserve.co.uk


I think it can sometimes be useful to regard a BLAST output file as a series of
pairwise alignments - and therefore it makes sense to add it to Bio.AlignIO and
another input file format.

http://biopython.org/wiki/AlignIO

Note that the AlignIO API will not allow any "clumping" of the pairwise
alignments (or HSPs in Blast terminology) according to the query or the target
sequence - you just get them all one after the other.

I will attach a rough Bio/AlignIO/BlastIO.py file which attempts to mimic the
naming conventions in the fasta-m10 parser.  This currently using Bio.Blast to
do the actual parsing, and then just using the Blast results to build alignment
objects with two sequences each.

I suggest using the format names "blast" and "blastxml" for the plain text and
XML output formats following BioPerl (although I would prefer "blast-xml" to
"blastxml"), see http://www.bioperl.org/wiki/HOWTO:SearchIO#Design


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