[Biopython-dev] [Biopython (old issues only) - Bug #2560] (Closed) Adding BLAST support to Bio.AlignIO

[redmine at redmine.open-bio.org]

Issue #2560 has been updated by Peter Cock.

Description updated
Status changed from New to Closed
% Done changed from 0 to 100

Superceeded with the introduction of Bio.SearchIO, closing issue.

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Bug #2560: Adding BLAST support to Bio.AlignIO
https://redmine.open-bio.org/issues/2560#change-15409

* Author: Peter Cock
* Status: Closed
* Priority: Normal
* Assignee: Biopython Dev Mailing List
* Category: Main Distribution
* Target version: Not Applicable
* URL: 
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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

---Files--------------------------------
BlastIO.py (6.28 KB)


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