[Bioperl-l] MSG: Response Error STACK: Error::throw when trying to download genbank files using GI

[Russell Smithies]

I think you'll only get the sequence back from the CDS feature so that may be the source of one of your first error, try adding a test:

                if ( $feat_object->primary_tag eq "CDS" ) {
                        my $sequence_string  = $feat_object->spliced_seq->seq;
                }

The second one is probably NCBI timing out. It's generally better to do a bulk download then post-process with BioPerl to avoid this problem.

--Russell


-----Original Message-----
From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-bounces at lists.open-bio.org] On Behalf Of Shaghayegh Hosseini
Sent: Saturday, 20 July 2013 1:29 a.m.
To: bioperl-l at bioperl.org
Subject: [Bioperl-l] MSG: Response Error STACK: Error::throw when trying to download genbank files using GI

Hi,

I am trying to fetch genebank features,here is the script


use strict;

use warnings;

use Bio::SeqIO;

use Bio::DB::EUtilities;

my $gi="385220095";

my  $factoryID = Bio::DB::EUtilities->new(-eutil => 'efetch',

                                          -db =>'protein',

                                          -rettype=> 'gbwithparts',

                                          -email=> 'x at y.com',

                                          -id=>$gi) ;

my $gbfile="$gi.gbk";

$factoryID->get_Response(-file =>$gbfile);

my $seqio_object = Bio::SeqIO->new(-file =>"$gbfile",'protein');

while ( my $seq_object=$seqio_object->next_seq){

    for my $feat_object ($seq_object->get_SeqFeatures) {

        my $sequence_string = $feat_object->spliced_seq->seq;

    }

}

I have got 2 problems

1. For some GIs I am getting (MSG: seq doesn' t validate, mismatch or MSG:
Got a sequence with no letters in it cannot guess alphabet )which is  annoying since I have about 2000 GIs  and for half of them this warnings are there BUT  it  does the job.

2. After  downloading lets say 1000 file I am getting Error (MSG: Response Error STACK: Error::throw or Bad Gateway)

Please let me know what I have done wrong

This  is the ERROR for First problem

--------------------- WARNING ---------------------

MSG: seq doesn't validate, mismatch is 266299291214720428459636348159

---------------------------------------------------


------------- EXCEPTION: Bio::Root::Exception -------------

MSG: Attempting to set the sequence to [266299291214720428459636348159] which does not look healthy

STACK: Error::throw

STACK: Bio::Root::Root::throw /Bioperl/1.6.1/lib/perl5/Bio/Root/Root.pm:368

STACK: Bio::PrimarySeq::seq /Bioperl/1.6.1/lib/perl5/Bio/PrimarySeq.pm:283

STACK: Bio::PrimarySeq::new Bioperl/1.6.1/lib/perl5/Bio/PrimarySeq.pm:234

STACK: Bio::Seq::new /Bioperl/1.6.1/lib/perl5/Bio/Seq.pm:497

STACK: Bio::SeqFeatureI::spliced_seq
/Bioperl/1.6.1/lib/perl5/Bio/SeqFeatureI.pm:618


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