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<FONT FACE="Calibri, Verdana, Helvetica, Arial"><SPAN STYLE='font-size:11pt'>Hi all<BR>
<BR>
I am trying to convert some transcript (cdna) coordinates to genome coordinates.<BR>
<BR>
below is my script to do so.<BR>
<BR>
my $gene_adaptor = $reg->get_adaptor( "human", "core", "gene" );<BR>
foreach my $geneid (keys %list){<BR>
my $gene = $gene_adaptor->fetch_by_stable_id($geneid); ####These are all valid ensembl gene ids<BR>
foreach my $transcript (@{$gene->get_all_Transcripts}){<BR>
my $ensID = $transcript->stable_id;<BR>
if (exists $list{$geneid}{$ensID}){<BR>
my $trmapper = $transcript->get_TranscriptMapper();<BR>
foreach my $loci (keys %{$list{$geneid}{$transcript->stable_id}}){<BR>
my @coords = $trmapper->cdna2genomic( $loci, $loci );<BR>
foreach my $coord (@coords){<BR>
print "$geneid\t".$transcript->stable_id ."\t$loci\t".$coord->id ."\t".$coord->start ."\t".$coord->end ."\t".$coord->stran ."\n";<BR>
}<BR>
}<BR>
}<BR>
}<BR>
}<BR>
However it is running into following error.<BR>
<BR>
MSG: 'Bio::EnsEMBL::DBSQL::TranscriptAdaptor' cannot be found.<BR>
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<BR>
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Translation.pm line 55, <F> line 1490.<BR>
Compilation failed in require at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 69, <F> line 1490.<BR>
BEGIN failed--compilation aborted at /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/TranscriptAdaptor.pm line 69, <F> line 1490.<BR>
Compilation failed in require at (eval 52) line 3, <F> line 1490.<BR>
<BR>
<BR>
FILE: Bio/EnsEMBL/Registry.pm LINE: 969<BR>
CALLED BY: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 892<BR>
Ensembl API version = 60<BR>
---------------------------------------------------<BR>
<BR>
-------------------- WARNING ----------------------<BR>
MSG: Could not find Transcript adaptor in the registry for homo_sapiens core<BR>
<BR>
FILE: EnsEMBL/DBSQL/DBAdaptor.pm LINE: 900<BR>
CALLED BY: Bio/EnsEMBL/Gene.pm LINE: 896<BR>
Ensembl API version = 60<BR>
---------------------------------------------------<BR>
<BR>
-------------------- EXCEPTION --------------------<BR>
MSG: Could not get adaptor Transcript for homo_sapiens core<BR>
<BR>
STACK Bio::EnsEMBL::DBSQL::DBAdaptor::AUTOLOAD /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/DBSQL/DBAdaptor.pm:905<BR>
STACK Bio::EnsEMBL::Gene::get_all_Transcripts /usr/lib/perl5/5.8.8/Ensembl/ensembl/modules/Bio/EnsEMBL/Gene.pm:896<BR>
STACK toplevel transcript2genome.pl:39<BR>
Ensembl API version = 60<BR>
---------------------------------------------------<BR>
<BR>
<BR>
having gone through translation.pm it seems that it is beginning to crash at the following line.<BR>
<BR>
use Scalar::Util qw(weaken);<BR>
<BR>
any ideas on why this could be happening.<BR>
<BR>
cheers<BR>
<BR>
-- <BR>
</SPAN><SPAN STYLE='font-size:12pt'>Hardip R. Patel<BR>
</SPAN><SPAN STYLE='font-size:11pt'>Bioinformatician, Molecular Genetics Division,<BR>
Victor Chang Cardiac Research Institute,<BR>
Darlinghurst, NSW – 2010, Australia<BR>
(W): +61 – 2 – 9295 8611<BR>
(M): 0449 180 715<BR>
<BR>
VCCRI 12th International Symposium <BR>
<FONT COLOR="#008FFE">“Charting the depths of RNA: from molecules to therapies”<BR>
</FONT>19 November 2010<BR>
visit <FONT COLOR="#0000FF"><U><a href="http://www.victorchang.edu.au">http://www.victorchang.edu.au</a></U></FONT> for details<BR>
<BR>
<BR>
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