[Bioperl-l] PSIBLAST parsing added to SearchIO::blastxml

Chris Fields cjfields at uiuc.edu
Thu Nov 29 18:06:42 EST 2007


For anyone using PSI-BLAST: I have implemented experimental PSI-BLAST  
parsing in Bio::SearchIO::blastxml (though it appears to be pretty  
stable!).  Since there isn't any easy way to distinguish between  
normal BLASTS and PSI-BLAST reports due to recent changes at NCBI to  
BLAST, you have to indicate how the report is to be parsed by passing  
in a '-blasttype' parameter:

$searchio = Bio::SearchIO->new('-tempfile' => 1,
        '-format' => 'blastxml',
        '-file'   => 'psiblast.xml',
        '-blasttype' => 'psiblast');

Otherwise it chunks the individual iterations out as separate BLAST  
reports and parses them as separate reports.

Tests have also been added to SearchIO.t.  I will update the HOWTO and  
blastxml docs soon.

chris


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