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

Jason Eric Stajich jason@cgt.mc.duke.edu
Wed, 31 Oct 2001 11:35:24 -0500 (EST)


Been down this road - I think if you specify -format => 'fasta' in
DB::Genbank initialization.  See the DB::GenBank documentation but it is
something like
my $db = new Bio::DB::GenBank(-format => 'Fasta');
my $seq = $db->get_Seq_by_acc('NT_004348');

If someone would go through and catalog the available retrieval methods
via the web with NCBI CGI parameters we can do a better job here.

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

> Hi,
> I was wondering, is it possible to get contigs from genbank, the refseq
> data?  I used a test script (right out of the tutorial), to get a sequence
> and write it to a file, it worked fine.  I then put in a refseq sequence and
> it failed with:
> Can't call method "_generic_seqfeature" on an undefined value at
> /usr/lib/perl5/site_perl/5.6.0/Bio/SeqIO/genbank.pm line 272.
> The following script worked fine, substitute something like NT_004348 for
> J00522 and it fails.  The accession number from the genbank file is
> #!/usr/local/bin/perl
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> $gb = new Bio::DB::GenBank();
> $seq1 = $gb->get_Seq_by_acc('J00522');
> $out = Bio::SeqIO->new('-file' => ">J00522.seq",
>                          '-format' => 'FASTA');
> $out->write_seq($seq1);
> I gave a half hearted effort to debug, but got lost.  Any errors I made
> easily noticed?  Or is refseq data not supported yet?
> -Mat
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

Jason Stajich
Duke University