[ensembl-dev] Transcript Adaptor

[Hardip Patel]

Hi all

I am trying to convert some transcript (cdna) coordinates to genome coordinates.

below is my script to do so.

my $gene_adaptor = $reg->get_adaptor( "human", "core", "gene" );
foreach my $geneid (keys %list){
  my $gene = $gene_adaptor->fetch_by_stable_id($geneid);  ####These are all valid ensembl gene ids
  foreach my $transcript (@{$gene->get_all_Transcripts}){
    my $ensID = $transcript->stable_id;
    if (exists $list{$geneid}{$ensID}){
      my $trmapper = $transcript->get_TranscriptMapper();
      foreach my $loci (keys %{$list{$geneid}{$transcript->stable_id}}){
    my @coords = $trmapper->cdna2genomic( $loci, $loci );
    foreach my $coord (@coords){
      print "$geneid\t".$transcript->stable_id ."\t$loci\t".$coord->id ."\t".$coord->start ."\t".$coord->end ."\t".$coord->stran ."\n";
    }
      }
    }
  }
}
However it is running into following error.

MSG: 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor' cannot be found.
Exception weaken is only available with the XS version of Scalar::Util at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Translation.pm line 55
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Translation.pm line 55, <F> line 1490.
Compilation failed in require at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 69, <F> line 1490.
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 69, <F> line 1490.
Compilation failed in require at (eval 52) line 3, <F> line 1490.


FILE: Bio/EnsEMBL/Registry.pm LINE: 969
CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm  LINE: 892
Ensembl API version = 60
---------------------------------------------------

-------------------- WARNING ----------------------
MSG: Could not find Transcript adaptor in the registry for homo_sapiens core

FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 900
CALLED BY: Bio/EnsEMBL/Gene.pm  LINE: 896
Ensembl API version = 60
---------------------------------------------------

-------------------- EXCEPTION --------------------
MSG: Could not get adaptor Transcript for homo_sapiens core

STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:905
STACK Bio::EnsEMBL::Gene::get_all_Transcripts /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Gene.pm:896
STACK toplevel transcript2genome.pl:39
Ensembl API version = 60
---------------------------------------------------


having gone through translation.pm it seems that it is beginning to crash at the following line.

use Scalar::Util qw(weaken);

any ideas on why this could be happening.

cheers

--
Hardip R. Patel
Bioinformatician, Molecular Genetics Division,
Victor Chang Cardiac Research Institute,
Darlinghurst, NSW - 2010, Australia
(W): +61 - 2 - 9295 8611
(M): 0449 180 715

VCCRI 12th International Symposium
"Charting the depths of RNA: from molecules to therapies"
19 November 2010
visit http://www.victorchang.edu.au for details


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