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Issue #2560 has been updated by Peter Cock.
<ul>
<li><strong>Description</strong> updated (<a title="View differences" href="https://redmine.open-bio.org/journals/diff/15409?detail_id=1765">diff</a>)</li>
<li><strong>Status</strong> changed from <i>New</i> to <i>Closed</i></li>
<li><strong>% Done</strong> changed from <i>0</i> to <i>100</i></li>
</ul>
<p>Superceeded with the introduction of Bio.SearchIO, closing issue.</p>
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<h1><a href="https://redmine.open-bio.org/issues/2560#change-15409">Bug #2560: Adding BLAST support to Bio.AlignIO</a></h1>
<ul><li>Author: Peter Cock</li>
<li>Status: Closed</li>
<li>Priority: Normal</li>
<li>Assignee: Biopython Dev Mailing List</li>
<li>Category: Main Distribution</li>
<li>Target version: Not Applicable</li>
<li>URL: </li></ul>
<p>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.</p>
<p><a class="external" href="http://biopython.org/wiki/AlignIO">http://biopython.org/wiki/AlignIO</a></p>
<p>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.</p>
<p>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.</p>
<p>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 <a class="external" href="http://www.bioperl.org/wiki/HOWTO:SearchIO#Design">http://www.bioperl.org/wiki/HOWTO:SearchIO#Design</a></p>
<fieldset class="attachments"><legend>Files</legend>
<a href="https://redmine.open-bio.org/attachments/download/980/BlastIO.py">BlastIO.py</a>
(6.28 KB)<br />
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