[Bioperl-l] desperate: what's wrong with this code

nkuipers nkuipers@uvic.ca
Sat, 16 Nov 2002 02:34:18 -0800


Hello all,

Normally I wouldn't whimp out like this but I am coming down to the wire and 
am relatively new to using bioperl.  I'll probably realize the problem as soon 
as I send it but wouldn't have without sending; you know how it goes. ;)  No 
output from following code.  Please offer your insight.  If there is no 
problem then I know the error lies in surrounding, non-bioperl methodology.  
Everything compiles and no runtime errors.  bioperl 1.02 with Perl 5.6.0 on 
Linux 7.2.  Many thanks!

Nathanael

#code snippet

use lib qw( /home/nkuipers/modules/lib/site_perl/5.6.0 );
use Bio::SearchIO;

open FH1, ">>output" or die $!;
open FH2, ">>bunk"   or die $!; #not really :)
my $parser = Bio::SearchIO->new( -file => $hashref->{infile}, -format => 
'blastxml' );
my $regex = qr/yaddayadda/;
while ( my $result = $parser->next_result ) {
     while ( my $hit = $result->next_hit ) {
          while ( my $hsp = $hit->next_hsp ) {
               if ( $hit->description =~ m/$regex/ ) {
                    print FH1 $result->query_name," hit ",$hit->name,"\n",
                              $hsp->query_string,"\n"
               } else {
                    print FH2 $result->query_name," hit ",$hit->name,"\n",
                              $hsp->query_string,"\n"
               }
           }
     }
}