[Bioperl-l] get_sequence() gets some sequences but not others

Chris Fields cjfields at uiuc.edu
Wed Jun 20 16:11:34 EDT 2007


I'm assuming you are using the Bio::Perl exported sub get_sequence 
().  I am able to reproduce the issue using bioperl-live; it's an odd  
issue as direct use of Bio::DB::GenPept works fine:

use Bio::DB::GenPept;

my $factory = Bio::DB::GenPept->new();

my @accs = qw(SKG3_YEAST NEM1_YEAST);

my $io = $factory->get_Stream_by_acc(\@accs);

while (my $seq = $io->next_seq) {
     print "Accession:",$seq->accession,"\n";
}

chris


On Jun 20, 2007, at 1:11 PM, Wollenberg, Kurt (NIH/NIAID) wrote:

> Greetings:
>
> I am working on a script to take a list of sequence IDs, extract the
> sequences from GenPept, and then run a BLAST search for each of the
> retrieved sequences. I am having a problem with the sequence  
> retrieval,
> where some sequences are found and others are not and it's not  
> obvious to me
> why this is.
>
> For example, using a text file containing the two following IDs as  
> input:
> SKG3_YEAST
> NEM1_YEAST
>
> My script
>
> while( <IN> ) {
>   chomp;
>   my $seqid = $_;
>   my $seq_obj = get_sequence( 'genpept', $seqid );
> }
>
> will create a sequence object for the first ID, (print "Accession of
> ",$seqid," is ",$seq_obj->accession, "\n"; gives me the correct  
> accession
> number) but for the second I am told
>
> -------------------- WARNING ---------------------
> MSG: id (NEM1_YEAST) does not exist
> ---------------------------------------------------
>
> When I pull up these records using the Entrez cross-databse search  
> in my web
> browser I find genpept records for both SKG3_YEAST and NEM1_YEAST  
> (using
> these search terms). In both records these IDs reside in the same  
> field
> ("DBSOURCE    swissprot: locus") so I'm mystified why get_sequence  
> finds one
> but not the other. Any advice would be greatly appreciated.
>
> Cheers,
> Kurt Wollenberg, Ph.D.
> Phylogenetics and Sequence Analysis Consultant
> Biocomputing Research Consulting Section
> Bioinformatics and Scientific IT Program (BSIP)
> NIH/NIAID/OTIS
> Contractor, Lockheed Martin
> http://bioinformatics.niaid.nih.gov
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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