[Bioperl-l] Help on retrieving NT contigs with Bio::DB::GenBank.

[Jason Eric Stajich]

Kun-

Has to do with NCBI retrieve of RefSeq contig (NT_*)  NCBI does not
implement this in the same way as 'regular' accession numbers.

This is discussed in previous messages in the list and should make its way
into a wiki FAQ at some point if someone wants to jump on it.

We're currently rethinking how to best provide this functionality as we
are essentially limited by NCBI not providing a single CGI-BIN which maps
to our simple Bio::DB::RandomAccessI interface for all valid accession
numbers.  Ideas and volunteers to take this on welcomed.  Mathew Wiepert
at Mayo started to look a it.  I suspect he got to the same point I did
which meant parsing HTML and doing a 2-step retrieval method, at which
point I balked.

-jason

On Fri, 30 Nov 2001, Kun Zhang wrote:

> Hello!
>
> I got a error message (attached below) when trying to retrieving some NT
> contigs from GenBank with the Bio::DB::Genbank module. It looks like the
> problem occurs only on NT sequence because the getGenBank.pl came with the
> bioperl-0.9.0 distribution works fine. And my perl script works when I
> replacing the "NT_001035" with "AF303112". Can anyone help me out? Thanks!
>
> Kun Zhang
> Human Genetics Center
> University of Texas-Houston
>
> ------------------------My codes-----------------------------
> my $gb = new Bio::DB::GenBank;
> $gb->request_format('fasta') ;
> $contigSeq = $gb->get_Seq_by_acc('NT_001035');
>
>
>
> ==============================ERROR MESSAGE==================================
> -------------------- EXCEPTION --------------------
> MSG: Attempting to set the sequence to [<HTML] which does not look healthy
> STACK Bio::PrimarySeq::seq
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/PrimarySeq.pm:251
> STACK Bio::PrimarySeq::new
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/PrimarySeq.pm:226
> STACK Bio::Seq::new /usr/local/lib/perl5/site_perl/5.6.1/Bio/Seq.pm:132
> STACK Bio::SeqIO::fasta::next_primary_seq
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/fasta.pm:130
> STACK Bio::SeqIO::fasta::next_seq
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/SeqIO/fasta.pm:85
> STACK Bio::DB::WebDBSeqI::get_Seq_by_acc
> /usr/local/lib/perl5/site_perl/5.6.1/Bio/DB/WebDBSeqI.pm:159
> STACK toplevel ./splitSeq.pl:26
>
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-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu