[Bioperl-l] a problem when using the Bioperl modules

Jason Stajich jason.stajich at ucr.edu
Mon Aug 23 11:58:07 EDT 2010

You haven't defined this variable $db - you need to not skip the part 
that initializes the Bio::DB::Fasta object that you had previous asked 
Please send all your future queries to the mailing list.

Guifeng Wei wrote, On 8/23/10 8:14 AM:
> Dear professor,
> after that, i revised my scripts, which is that i divide the genomic 
> sequences into 7 single file, every file contains the sequence from a 
> chromosome.
> however, when i try to run the scripts, the following error was coming.
> Can't call method "seq" on an undefined value at bed_to_fasta.pl 
> <http://bed_to_fasta.pl> line 29, <IN> line 1.
> while(<IN>){
>         chomp $_;
>         my @bed=split(/\s+/, $_ );
>     #print length($db->seq('chrI'));
>         my $chr_id=$bed[0];
>         my $start=$bed[1];
>         my $end=$bed[2];
>         my $seq_name=$bed[3];
>         my $strand=$bed[5];
> my $segment =  $db ->seq($chr_id,$start=>$end);
>         print ">",$seq_name,"_",$chr_id,":",$start=>$end;
>         print "$segment\n";
> }
> the blue line is .
> why?

Jason E. Stajich, PhD
Assistant Professor
Department of Plant Pathology & Microbiology
University of California
Riverside, CA 92521
jason.stajich at ucr.edu
office: 951.827.2363



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