: [Bioperl-l] Bio::DB::Query::GenBank retrieves fewer sequences than Webbrowser query

T.D. Houfek tdhoufek at unity.ncsu.edu
Wed Mar 24 16:54:19 EST 2004


Just for kicks I tried to duplicate the problem (I get the same number
of sequences from NCBI's web sequin tool as Jrgen, but using the
Bio::DB::Query:Genbank method I get 644 sequences (not less than 100,
but not the 5000+ we are expecting).  Placing an escape backslash before
the brackets does not seem to help me:

--- my test script below ---

use strict;
use Bio::DB::GenBank;
use Bio::DB::Query::GenBank;
my $gb=new
my $query = Bio::DB::Query::GenBank->new
        (-query => 'Mus\[Organism] AND exon NOT mRNA NOT cDNA',
         -db => 'Nucleotide');
my $seqio = $gb->get_Stream_by_query($query);
my $numresults=0;
while( my $seq = $seqio->next_seq ) { $numresults++; }
print "Num results: $numresults\n";


 T.D. Houfek
 Tobacco Genome Initiative
 NCSU, Raleigh, NC 27606

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