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I am trying to use an external file with a list of gene names to query the ENSEMBL IDs using the perl API. This script works:

#!/usr/local/bin/perl

use strict;
use warnings;
use Bio::Ensembl::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'useastdb.ensembl.org',
    -port => 5306,
    -user => 'anonymous'
);

my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );

my @genes;
@genes = ('CCL2', 'CCL5');

foreach $name(@genes){
    my $gene = $gene_adaptor -> fetch_by_display_label($name);
    print "GENE ", $gene->stable_id(), ",";
}

However I can't figure out how to get this to work with an external file that contains a list of genes like this:

genes.txt

CCL2
CCL5

Here's what I tried:

#!/usr/local/bin/perl

use strict;
use warnings;
use Bio::Ensembl::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

$registry->load_registry_from_db(
    -host => 'useastdb.ensembl.org',
    -port => 5306,
    -user => 'anonymous'
    );

my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );

open (IDs, '<', "genes.txt") or die "can't read input file";
while (<IDs>){
    my $gene = $gene_adaptor -> fetch_by_display_label($_);
    print "GENE ", $gene->stable_id(), ",";
}

But I'm getting this error: Can't call method "stable_id" on an undefined value at ./get_ensembl_ids.pl line 22, <IDs> line 1.

I was trying to follow this tutorial for reading txt files in perl, but what am I missing for getting perl to actually fetch the ENSEMBL ids with each of the .txt file lines?

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Similar to reading files in other languages, it is necessary to trim the newlines from each line. If you add chomp; to the first line of the while loop, the code runs just fine (note that I also print a newline at the end of the loop).

open (IDs, '<', "genes.txt") or die "can't read input file";
while (<IDs>){ 
    chomp;
    my $gene = $gene_adaptor -> fetch_by_display_label($_);
    print "GENE ", $gene->stable_id(), ",";
}
print '\n';

The new loop produces the following result:

>$ perl query.pl 
GENE ENSG00000108691,GENE ENSG00000271503,

Additionally, you may need to catch any exceptions/errors thrown if you have an invalid gene in your input file:

open (IDs, '<', "genes.txt") or die "can't read input file";
while (<IDs>){ 
    chomp;
    eval {
        my $gene = $gene_adaptor -> fetch_by_display_label($_);
        print "GENE ", $gene->stable_id(), ",";
    };
    if ($@) {
        warn "Error:\t$@\n"
    }
}
print '\n';
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  • $\begingroup$ Thanks @Throckmorton for the response. Your code is still throwing the error at me, but manages to retrieve the Ensembl ID for CCL5: Error: Can't call method "stable_id" on an undefined value at ./get_ensembl_ids.pl line 20, <IDs> line 1. GENE ENSG00000271503,\n% Any idea why that might be? Can I ask what version of perl you're using? $\endgroup$ Jul 13 at 15:45
  • $\begingroup$ I am running 5.26 $\endgroup$ Jul 14 at 21:57
  • $\begingroup$ @user45678789 I will say it is a bit suspicious that you have use Bio::Ensembl::Registry; as well as my $registry = 'Bio::EnsEMBL::Registry';, I would assume the case should be the same in both lines. $\endgroup$ Jul 15 at 1:30

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