[ensembl-dev] gene to coords code issue

[Sean O'Keeffe]

Thanks for the response Javier.

I see the reference to an array of objects and I've implemented this.
However I don't get it. The script dies at the call to
fetch_all_by_external_name() - Can't call method
"fetch_all_by_external_name" on an undefined value.
It never gets to implement the loop of array objects. The $variable $id is
valid and prints out prior to the script dying.

...
print $id,"\n";
my $adaptor = $registry->get_adaptor( 'Human', 'Core', 'gene' );

my $gene = $adaptor->fetch_all_by_external_name($id);

  foreach $g(@$gene){
    $chr = $g->seq_region_name();
    $start = $g->seq_region_start();
    $end = $g->seq_region_end();
    print OUT join("\t", $chr,$start,$end,$id),"\n";
  }


On 20 April 2012 00:49, Javier Herrero <jherrero at ebi.ac.uk> wrote:

>  Dear Sean
>
> The method fetch_all_by_external_name returns a reference to an array of
> Bio::EnsEMBL::Gene objects. All the methods named "fetch_all_by..." return
> a reference to an array. The array might be empty or contain just one
> entry, but you will always get a reference to an array. Contrarily, all the
> methods named "fetch_by..." return either undef or 1 single object.
>
> Typically, you would use a foreach loop to go through all possible
> returned object:
>
>
> open OUT, ">$gene_file.coords";
> for my $geneid ( @unique ) {
>     chomp $geneid;
>     ensembl_coords($geneid);
> }
>
> sub ensembl_coords {
>   my ($id) = @_;
>
>   my $adaptor = $registry->get_adaptor( 'Human', 'Core', 'gene' );
>
>   my $all_genes = $adaptor->fetch_all_by_external_name($id);
>
>   foreach my $gene (@$all_genes) {
>
>     $chr = $gene->seq_region_name();
>     $start = $gene->seq_region_start();
>     $end = $gene->seq_region_end();
>      print OUT join("\t", $chr,$start,$end,$id),"\n"; #I have added the
> original $id here
>    }
>
> }
>
>
> I hope the helps
>
> Javier
>
>
>
>
> On 20/04/12 04:49, Sean O'Keeffe wrote:
>
> Hi,
> I've used the code below on multiple occasions to convert external gene
> names to chromosome coords and it worked fine.
> However when I tried it just now I get the error for the very first gene
> DNAI2 and the script crashes:
>
>  Can't call method "seq_region_name" on unblessed reference
>
>  When I tried fetch_by_display_label($id) - I get:
>
>  Can't call method "seq_region_name" on an undefined value
>
>  Have I missed something?
> Thanks for any help,
> Sean.
>
>  p.s. I tried connecting to the useastdb.ensembl.org,<http://useastdb.ensembl.org/>as I'm in the states, but It gave the following (maybe the 2 issues are
> related):
>
>  DBI connect('host=useastdb.ensembl.org;port=3306','anonymous',...)
> failed: Can't connect to MySQL server on 'useastdb.ensembl.org' (111) at
> /home/sean/tools/ensembl_53/modules/Bio/EnsEMBL/Registry.pm line 1329
> Can't call method "selectall_arrayref" on an undefined value at
> /home/sean/tools/ensembl_53/modules/Bio/EnsEMBL/Registry.pm line 1332.
>
>  ==============
>
>  #!/usr/bin/perl
>
>  use strict;
> use lib '/home/sean/tools/ensembl_53/modules';
>
>  use Bio::SeqIO;
> use Bio::Root::IO;
> use Bio::EnsEMBL::DBSQL::BaseAdaptor;
>  use Bio::EnsEMBL::Registry;
>
> my $registry = 'Bio::EnsEMBL::Registry';
> #$registry->load_registry_from_db(-host => 'useastdb.ensembl.org',-user
> => 'anonymous');
> $registry->load_registry_from_db(-host => 'ensembldb.ensembl.org',-user
> => 'anonymous');
>
> open OUT, ">$gene_file.coords";
> for my $geneid ( @unique ) {
>     chomp $geneid;
>     ($chr,$start, $end) = ensembl_coords($geneid);
>     print OUT join("\t", $chr,$start,$end,$geneid),"\n";
>  }
>
> sub ensembl_coords {
>   my ($id) = @_;
>
>   my $adaptor = $registry->get_adaptor( 'Human', 'Core', 'gene' );
>
>   my $gene = $adaptor->fetch_all_by_external_name($id);
>   # my $gene = $adaptor->fetch_by_display_label($id);
>
>    $chr = $gene->seq_region_name();
>   $start = $gene->seq_region_start();
>   $end = $gene->seq_region_end();
>   return ($chr,$start,$end);
>
>  }
>
>
> _______________________________________________
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>
>
> --
> Javier Herrero, PhD
> Ensembl Coordinator and Ensembl Compara Project Leader
> European Bioinformatics Institute (EMBL-EBI)
> Wellcome Trust Genome Campus, Hinxton
> Cambridge - CB10 1SD - UK
>
>
> _______________________________________________
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> Ensembl Blog: http://www.ensembl.info/
>
>
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