Entering edit mode
6.3 years ago
Hello all,
My previously working perl script to fetch a given region suddenly has failed. I use the Bio::DB::EUtilities library as shown below.
use strict;
use warnings;
use Bio::DB::EUtilities;
my $result = Bio::DB::EUtilities->new( -eutil => 'efetch',
-db => 'nucleotide',
-rettype => 'gb',
-email => 'validemail@gmail.com'
);
$result->set_parameters( -id => '568815579',
-seq_start => '1',
-seq_stop => '100',
-strand => '2'
);
$result->get_Response(-file => 'result.gb');
However, the above code works if I change the "rettype" parameter from gb to fasta. I tried the web (URL) version to debug and I noticed similar behavior. The same URL with FASTA as rettype worked, but if the rettype was changed to gb it failed with a bad gateway error.
This URL below works for the FASTA format
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=568815579&strand=2&seq_start=1&seq_stop=100&rettype=fasta&retmode=text
This URL for GB format fails with a Bad Gateway error after a few minutes
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nuccore&id=568815579&strand=2&seq_start=1&seq_stop=100&rettype=gb&retmode=text
Can some one please advice on what I'm doing wrong, or if anything has changed recently in efetch usage?
Thank you
Senthil