[Bioperl-l] Getting refseq (contigs) from Genbank

[Jason Eric Stajich]

Guess they've changed Entrez CGI somehow - turn debugging on
(initialize with -verbose=> 1) and see what the whole HTML msg is that is
being returned.


On Wed, 31 Oct 2001, Wiepert, Mathieu wrote:

> Jason,
> Thanks for the help, still no luck?  I tried this now
>
> #!/usr/local/bin/perl
> use Bio::DB::GenBank;
> use Bio::SeqIO;
>
> $gb = new Bio::DB::GenBank(-retrievaltype => 'tempfile' ,
>                                -format => 'Fasta');
> $gb->request_format('fasta');
> my $seq = $gb->get_Seq_by_acc('NT_004348');
>
> $out = Bio::SeqIO->new('-file' => ">NT_004348.seq",
>                          '-format' => 'fasta');
> $out->write_seq($seq);
>
> But get:
> -------------------- EXCEPTION --------------------
> MSG: Attempting to set the sequence to [<html] which does not look healthy
> STACK Bio::PrimarySeq::seq
> /usr/lib/perl5/site_perl/5.6.0/Bio/PrimarySeq.pm:243
> STACK Bio::PrimarySeq::new
> /usr/lib/perl5/site_perl/5.6.0/Bio/PrimarySeq.pm:218
> STACK Bio::Seq::new /usr/lib/perl5/site_perl/5.6.0/Bio/Seq.pm:132
> STACK Bio::SeqIO::fasta::next_primary_seq
> /usr/lib/perl5/site_perl/5.6.0/Bio/SeqIO/fasta.pm:130
> STACK Bio::SeqIO::fasta::next_seq
> /usr/lib/perl5/site_perl/5.6.0/Bio/SeqIO/fasta.pm:85
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/lib/perl5/site_perl/5.6.0/Bio/DB/WebDBSeqI.pm:159
> STACK toplevel getcontigs.pl:8
> -------------------------------------------
>
> I tried with and without the $gb->request_format('fasta'); line, same error.
> I got that from the help on DB::GenBank
>
> "Note that when querying for GenBank accessions starting with 'NT_' you will
> need to call $gb->request_format('fasta') beforehand, because in GenBank
> format (the default) the sequence part will be left out (the reason is that
> NT contigs are rather annotation with references to clones). "
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu