[Bioperl-l] Bio::DB::Query::GenBank

[Lincoln Stein]

This exact example used to work.  If it doesn't work now it is because NCBI 
has once more changed something in their "published stable" interface.  I 
will look into it, but I can't guarantee that this functionality will be 
restored.  If it doesn't, the GenBank query interface will again be removed 
from BioPerl, probably permanently this time.

Lincoln

On Tuesday 06 May 2003 03:46 pm, Josh Lauricha wrote:
> Using the following code (From the Bio::DB::Query::GenBank doc):
> #!/usr/bin/perl -w
> use Bio::DB::GenBank;
> use Bio::SeqIO;
> use strict;
>
> my $gb     = new Bio::DB::GenBank;
> my $seqin  = new Bio::SeqIO(-format => 'efa');
> my $seqout = new Bio::SeqIO(-format => 'efa');
>
> my $seqio = $gb->get_Stream_by_query('Oryza sativa[Organism] AND EST');
>
> while( my $seq =  $seqio->next_seq ) {
> 	            print "seq length is ", $seq->length,"\n";
> }
>
> I get the following error:
> Warning(s) from GenBank:
>                 <FieldNotFound>Organism</FieldNotFound>
>
> However, if I goto www.ncbi.nih.gov and type in:
> 'Oryza sativa[Organism] AND EST'
> I get something around 18k hits in both the nucleotide and protien
> databases.
>
> I need to find more information about some sequences, I hope to find
> their gi numbers. However, none of the data I have is specific to the
> genes, so my thought was to search for the org name the seq are from,
> then to compare the seq from genbank to the ones I have.
>
> I have:
> 1) An accession number that seems to be the GenBank LOCUS id, which
>    is not a valid search field.
> 2) A nick name similar to SWProt's, but not identical.
> 3) For most, a SWProt accession
> 4) A description.
> 5) The sequence.
>
> Any ideas on why the query didn't work or a better way to get the GIs
> than just searching by hand?
>
> Thanks,
> Josh Lauricha
>
>
>
>
>
>
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-- 
Lincoln Stein
lstein at cshl.org
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)