[Bioperl-l] bl2seq and next_aln()

Gregory Drake Wilson gdw1 at cornell.edu
Wed Aug 3 12:00:13 EDT 2005

I am trying to parse a bl2seq file but am only being returned one of the
alignments when there are 2+.
        my @params = (program  => 'blastn' , 'outfile' => 'bl2seq.out');
        my $factory = Bio::Tools::Run::StandAloneBlast->new(@params);
        my $report = $factory->bl2seq($seq1, $seq2);

        my $str = Bio::AlignIO->new(-file=> 'bl2seq.out','-format' =>

        while ( my $aln = $str->next_aln() ) {
           print $aln->consensus_iupac()."\n";

Opening 'bl2seq.out' shows mutiple alignments, yet this code only returns
the first one in the file. Any thoughts?


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