[Bioperl-l] problem with a script

[Robert Buels]

1.) You need to use strict.  Always have use strict at the top of your 
code.  That would have caught this error.
2.) The proximate problem here is that your searchio object is call 
$searchio, while you are calling $in->next_result.  You want 
$searchio->next_result instead.

Rob

Joonas Jämsen wrote:
> Hi,
> 
> Im trying to run the script below and I get an error: "Can't call method "next_result" on an undefined value at parser.pl line 5."
> 
> 
> #!/v/linux26_x86_64/appl/molbio/bioperl/perl/bin/
> use Bio::SearchIO
> my $searchio = Bio::SearchIO->new(-format => 'hmmer', -file   => '/wrk/xxxx/hmm/hmmsearch_nr.out');
> while ( my $result = $in->next_result ) {
>      while ( my $hit = $result->next_hit ) {
>          while ( my $hsp-evalue<=10 ) {
>              while ( my $hsp = $hit->next_hsp ) {
>                  print $hit->accession(), "\n";
>          }
>      }
>  }
> 
> Could someone tell me what is wrong?
> 
> Thanks.
> 
> 
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