[Bioperl-l] Weird efetch problem.

shalabh sharma shalabh.sharma7 at gmail.com
Wed Apr 4 17:24:08 EDT 2012


Hi All,
        I am facing a really weird problem using efetch. I am getting
different outputs if i am using different method of passing values.

Like if i am using this method:

#!/usr/bin/perl -w
use Bio::DB::EUtilities;
use Bio::SeqIO;
my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                                       -db      => 'protein',
                                       -rettype => 'fasta',
                                       -email   => 'ssharmai at uga.edu',
                                       -id      => '256009369');

my $file = 'genome.fasta';
$factory->get_Response(-file => $file);

I am getting correct protein sequence but if i am passing values (same id)
via an array i am getting nucleotide sequences.

use Bio::DB::EUtilities;
use Bio::SeqIO;
my @ids;
my $c = 0;
open(IN,"$ARGV[0]");
while(<IN>){
      my $id = $_;
      chomp($id);chop($id);
      $ids[$c] = $id;
      print "$id\n";
      $c++;
}
close(IN);
my $factory = Bio::DB::EUtilities->new(-eutil   => 'efetch',
                                       -db      => 'protein',
                                       -rettype => 'fasta',
                                       -email   => 'ssharmai at uga.edu',
                                       -id      => \@ids);

my $file = 'genome.fasta';

Thanks
Shalabh

-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636


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