[Bioperl-l] Bio::DB::Fasta

Jason Stajich jason at bioperl.org
Tue Jun 5 23:12:40 EDT 2007


the file handle is probably not important, Perl just reports this if  
there is a filehandle open.

more importantly what is on line 84....

my guess is you are trying to get a sequence out and it doesn't exist  
- some error code around the lines getting the sequence out would be  
helpful.


On Jun 5, 2007, at 7:00 PM, Staffa, Nick (NIH/NIEHS) wrote:

> I am wondering if I knew what this error message exactly meant, if  
> I could
> discern my error.
> I don't see much difference in this program and programs that worked.
> Can I assume that the new worked because an index file exists?
> I don't know how the filehandle UTR_TT_GENES gets involved.
> Maybe I should use some other module, but I really would like to have
> get_Seq_by_id functionality.
>
> The error message:
> Dpse ortholog = Dpse_GA17307
> fetching GA17307
> Can't call method "seq" on an undefined value at Match-emNEWTEST.pl  
> line 84,
> <UTR_TT_GENES> line 4.
>
> Relevant code:
> #!/usr/bin/perl
> #
> #
> #
> use strict;
> use Bio::DB::Fasta;
> use Bio::Tools::SeqWords;
> use Bio::Seq;
> use Bio::SeqIO;
> #
> my $db =
> Bio::DB::Fasta->new('/home/staffa/clients/Kari/D_pse_genome/testit/ 
> TT_orthol
> ogs_Dpse_genes.fa',
>                                 -makeid => \&make_my_id);
> ...
> ...
> ...
> my $pse_obj = $db->get_Seq_by_id('GA17307');
> my $pse_sequence = $pse_obj->seq;
>
>
>
>
> Nick Staffa
> Telephone: 919-316-4569  (NIEHS: 6-4569)
> Scientific Computing Support Group
> NIEHS Information Technology Support Services Contract
> (Science Task Monitor: John D. Grovenstein (grovens1 at niehs.nih.gov)
> National Institute of Environmental Health Sciences
> National Institutes of Health
> Research Triangle Park, North Carolina
>
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l

--
Jason Stajich
jason at bioperl.org
http://jason.open-bio.org/


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