[Bioperl-guts-l] [Bug 3018] New: no homology_string or seq_inds output using Bio::SearchIO::gmap_f9

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Wed Mar 3 16:24:49 EST 2010


http://bugzilla.open-bio.org/show_bug.cgi?id=3018

           Summary: no homology_string or seq_inds output using
                    Bio::SearchIO::gmap_f9
           Product: BioPerl
           Version: 1.6 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P3
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: mukhyala at gene.com


the homology_string and seq_inds methods do not return any output when using
Bio::SearchIO::gmap_f9.

Here's the code to reproduce the problem:

my $sio = new Bio::SearchIO(-format=>"gmap_f9",-file=>"t/data/gmap_f9.txt");
my $result = $sio->next_result;
my $hit = $result->next_hit;
my $hsp = $hit->next_hsp;
print $hsp->homology_string,"\n";
print "\n", $hsp->seq_inds('query', 'gap');

The input file t/data/gmap_f9.txt is the same file used in gmap_f9.t test
script included in bioperl 1.6.
I will attach a bug fix for the module and the test script.


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