[Bioperl-l] get_stream_by_batch with an invalid ac

[Lincoln Stein]

Version 1.2 of Bioperl will use NCBI's new interface, and this problem may 
possibly  go away.

Lincoln

On Wednesday 07 August 2002 08:13 am, Mick Watson wrote:
> Hi
>
> This isn't a bioperl problem, it's an issue with the NCBI.  All bioperl
> does is provide the ability to query the NCBI, and therefore bioperl's
> behaviour will be exactly the same as the NCBI's
>
> If you go to http://www.ncbi.nlm.nih.gov/ and enter "AC013798 AC013798
> AC021953 ZZ99999" into the query box at the top, and press Go then you
> will see that the query returns no results.  If you remove the ZZ99999
> from the list then the NCBI will return the results.
>
> So Bioperl is simply providing you with exactly what the NCBI does i.e.
> a batch query system that doesn't accept invalid accessions.  It is the
> NCBI who need to improve their query interface
>
> Thanks
> Mick
>
> michael wrote:
> >	As I understand it if I want to fetch a lot of sequences
> >by accession number I should use get_stream_by_batch.  However if I
> >have an invalid accession number in the 'fetch list' I can't seem to
> >access any of the returned data.
> >
> >	If I run the script below with two (valid) accession numbers
> >(['AC013798', 'AC021953']) I get:-
> >
> >1 gi|7382144|gb|AC013798.4|AC013798
> >2 gi|7283183|gb|AC021953.3|AC021953
> >Can't call method "display_id" on an undefined value at b.pl line 18,
> ><GEN1> line 2.
> >
> >	Which is more or less what I'd expect using (['AC013798',
> >'AC021953', 'ZZ99999']) I get:-
> >
> >Can't call method "display_id" on an undefined value at b.pl line 11.
> >
> >	Thinking that the null value from the ZZ99999 is at the start of
> >the results array (on something) I tried a sacrificial call on display_id
> >(by commenting out the print "1 " line) but it fails at the next call
> >
> >Can't call method "display_id" on an undefined value at b.pl line 14.
> >
> >	Am I missing something?
> >
> >
> >#!/usr/bin/perl -w
> >use strict;
> >use Bio::DB::GenBank;
> >
> >my $gb = new Bio::DB::GenBank;
> >my $seqio = $gb->get_Stream_by_acc(['AC013798', 'AC021953', 'ZZ99999']);
> >
> >my $clone =  $seqio->next_seq;
> >print "1 ", $clone->display_id,"\n";
> >
> >$clone =  $seqio->next_seq;
> >print "2 ", $clone->display_id,"\n";
> >
> >$clone =  $seqio->next_seq;
> >print "3 ", $clone->display_id,"\n";
> >
> >
> >
> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >Michael John Lush PhD		 	 Tel:44-20-7679-5027
> >Nomenclature Bioinformatics Support 	 Fax:44-20-7387-3496
> >HUGO Gene Nomenclature Committee Email:  nome@galton.ucl.ac.uk
> >The Galton Laboratory
> >University College London, UK
> >URL: http://www.gene.ucl.ac.uk/nomenclature/
> >~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> >
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>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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