[Bioperl-guts-l] [Bug 2427] New: error while using Bio::Search::cross_match

bugzilla-daemon at portal.open-bio.org bugzilla-daemon at portal.open-bio.org
Thu Jan 3 07:24:18 EST 2008


           Summary: error while using Bio::Search::cross_match
           Product: BioPerl
           Version: 1.5 branch
          Platform: PC
        OS/Version: Linux
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Bio::Search/Bio::SearchIO
        AssignedTo: bioperl-guts-l at bioperl.org
        ReportedBy: massocec at yahoo.fr

I want to use the parser for cross_match results files Bio::Search::cross_match
but it returns no result when running on my example file. 

My code is the same that in the documentation example :
use strict;
use Bio::SearchIO::cross_match;
use Data::Dumper;

 # Working with iterations (CrossMatch results)
    my $searchIO = Bio::SearchIO->new( -format => 'cross_match',
                            -file   => "$file.screen.out" )
    while(my $r = $searchIO->next_result) {
      while(my $hit = $r->next_hit) {
        while(my $hsp = $hit->next_hsp) {
           #Do the processing here.
           print Dumper($hsp);              

when executing the programm nothig is return.
(attached my croos_match result file)

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