[ensembl-dev] issue with my script to fetch genes from a file using API

[Nathalie Conte]

HI, I have a file see format attached
basically the coordinates of the regions I want to retrieve genes from 
are column 1( chromosome) 5(start) and 6(end)
I used this script to parse through the file and give my external gene 
names , in the output I get only 1 gene name and a message:
Can't call method "get_all_Genes" on an undefined value at 
./fetch_gene_API.pl line 34.
I don't understand where this comes from , I wanted to check whether you 
could help/advise
thanks
Nathalie

#!/software/bin/perl
use warnings;
use strict;
use Bio::EnsEMBL::Registry;
use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
#use lib "/nfs/team82/nac/amy/may2011/lib";

my $registry = "Bio::EnsEMBL::Registry";
$registry->load_registry_from_db(-host => 'ensembldb.ensembl.org', -user 
=> 'anonymous');
my $file = 
"/nfs/team82/nac/Roland/November_2011/PT_mcrs0.25T_50_2_20M_sdundo.bind_API.txt";

unless (open(REGIONS, $file)){
        print "Cannot open file \"$file\"\n\n";
}

my @regions = <REGIONS>;

close REGIONS;
open(OUT,">PT_mcrs0.25T_50_2_20M_sdundo.bind_API_fetchGene.txt");
my $slice_adaptor = $registry->get_adaptor('Mouse', 'Core', 'Slice');

foreach my $region(@regions){
       chomp $region;

        my @coordinates = split(/\t/, $region);

        my $chromosome = $coordinates[0];
        my $start = $coordinates[4];
        my $end = $coordinates[5];

my $slice = $slice_adaptor->fetch_by_region('chromosome',$chromosome, 
$start, $end);


 my $genes = $slice->get_all_Genes;
foreach my $gene( @{$genes} ){
   
  print OUT 
$coordinates[0],"\t",$coordinates[1],"\t",$coordinates[2],"\t",$coordinates[3],"\t",$coordinates[4],"\t",$coordinates[5],"\t",$gene->external_name,"\t",$coordinates[6], 
"\n";

}
}
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