Question: Bioperl Bio::Db::Entrezgene No Longer Works
0
gravatar for Matt LaFave
6.8 years ago by
Matt LaFave290
San Diego, CA
Matt LaFave290 wrote:

I've been using BioPerl's Bio::DB::EntrezGene module to retrieve Entrez gene names given the numerical ID. This worked fine for months, and as recently as two weeks ago. Recently, though, it only returns an error. The strangest thing (to me) is that this happens even if I just run the sample code from the documentation. For example, if I run this:

#!/usr/bin/perl

use strict;
use warnings;
use Bio::DB::EntrezGene;

my $db = Bio::DB::EntrezGene->new;

my $seqio = $db->get_Stream_by_id([2, 4693, 3064]); # Gene ids
    while ( my $seq = $seqio->next_seq ) {
            print "id is ", $seq->display_id, "\n";
    }

exit;

I get this:

Replacement list is longer than search list at /Library/Perl/5.12/Bio/Range.pm line 251.
UNIVERSAL->import is deprecated and will be removed in a future perl at /Library/Perl/5.12/Bio/Tree/TreeFunctionsI.pm line 94
Data Error: none conforming data found on line 1 in /var/folders/2f/55z0d46n3l10bq650j6svgw89rmqw1/T/mkguvw1MOO/VR86iPUDSJ!
first 20 (or till end of input) characters including the non-conforming data:
::= {
  {
    track-
 at /Library/Perl/5.12/Bio/SeqIO/entrezgene.pm line 171

If anyone has any ideas about what might be going on & how to fix it, it'd be much appreciated. Thanks!

bioperl • 1.5k views
ADD COMMENTlink modified 6.8 years ago by Istvan Albert ♦♦ 82k • written 6.8 years ago by Matt LaFave290
1

Seems like this was answered in the comments at StackOverflow: http://stackoverflow.com/questions/16199037/bioperl-module-biodbentrezgene-no-longer-working.

ADD REPLYlink written 6.8 years ago by Neilfws48k
0
gravatar for Istvan Albert
6.8 years ago by
Istvan Albert ♦♦ 82k
University Park, USA
Istvan Albert ♦♦ 82k wrote:

As Neilfws points out

Seems like this was answered in the comments at StackOverflow: http://stackoverflow.com/questions/16199037/bioperl-module-biodbentrezgene-no-longer-working.

adding this so that it shows up as answered.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by Istvan Albert ♦♦ 82k
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