[Bioperl-l] Query gene identifiers from mouse and use homologene to return human orthologues

Mark Aquino maquino at knome.com
Tue Oct 11 10:44:06 EDT 2011


Hi,

I'm trying to run a perl script that will, as the subject says, convert a list of mouse gene ids to their human orthologues.  However, my code crashes and I've been unable to see if I'm even on the right track in going about doing this so any help would be appreciated.

Code:

#!/usr/bin/perl
use strict;
use warnings;
use Bio::DB::EUtilities;
my $esearch = Bio::DB::EUtilities->new(-eutil => 'esearch',
                                        -db => 'homologene',
                                        -term => 'Copg AND mouse',
                                        -usehistory => 'y');
$esearch->get_Response || die;
my @h_genes = $esearch->get_ids;
print "@h_genes\n";
my $history = $esearch->next_History || die "elink failed";
my $elink = Bio::DB::EUtilities->new(-eutil => 'elink',
                                        -history => $history,
                                        -cmd => 'neighbor_history');

$elink->get_Response;
my $hist1 = $elink->next_History;
my $esum = Bio::DB::EUtilities->new(-eutil => 'esummary',
                                        -history => $hist1,
                                        -cookie => $elink->next_cookie);
$esum->get_Response || die "esum failed";
while (my $docsum = $esum->next_DocSum){
        print $docsum->get_id,"\n";
        print "TaxID: ", $docsum->get_Content_by_name('TaxID'),"\n";
}

[According to what I can find, the method get_Content_by_name should work but I am getting the error:
Throws: Can't locate object method "get_Content_by_name" via package "Bio::Tools::EUtilities::Summary::DocSum" at testeutil.pl line 67.]





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