Hi. I'm running ActivePerl 5.6 on Windows 2000. I installed the Boulder
module from CPAN and I'm trying to access Genbank using Boulder::Genbank via
Entrez. I'm able to retrieve the correct entries by query, but it keeps
retrieving them over and over in an infinite loop. Maybe you can see what
I'm doing wrong? Here is the code:
use Boulder::Genbank;
$a = "courant_nrdb.txt"; #output file for query results
$query = 'Neolamprologus brichardi[Organism]';
$gb = Boulder::Genbank->newFh(-accessor => 'Entrez',
-query => $query,
-db => 'n');
open(OUT, ">$a") || die "cannot create a: $!";
while ($data = <$gb>)
{
print "entry retrieved\n"; #Telling me it got an entry (It's
repeating infinitely)
$gi = $data->Nid;
$gi =~ s/\D//g; #Get rid of first letter in GI entry
#Now print the entry in FASTA format
print OUT ">gi|$gi|gb|";
print OUT $data->Version;
print OUT "|";
print OUT $data->Accession;
print OUT " ";
print OUT $data->Definition;
print OUT "\n";
print OUT $data->Sequence;
print OUT "\n";
}
close OUT;
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