[ensembl-dev] FW: ensembl api query
BURT David
dave.burt at roslin.ed.ac.uk
Sat Jun 11 15:03:12 BST 2011
Recently ran a "simple" test of my Ensembl perl api install using an example from the core tutorial - to list external database entries.
Perl program and output is attached and below.
PERL SCRIPT
==========
#!/bin/perl.exe -w
use strict;
use Bio::EnsEMBL::Registry;
my $registry = 'Bio::EnsEMBL::Registry';
$registry->load_all();
# Define a helper subroutine to print DBEntries
sub print_DBEntries
{
my $db_entries = shift;
foreach my $dbe ( @{$db_entries} ) {
printf "\tXREF %s (%s)\n", $dbe->display_id(), $dbe->dbname();
}
}
my $gene_adaptor = $registry->get_adaptor( 'Human', 'Core', 'Gene' );
# Get the 'COG6' gene from human
my $gene = $gene_adaptor->fetch_by_display_label('COG6');
print "GENE ", $gene->stable_id(), "\n";
print_DBEntries( $gene->get_all_DBEntries() );
foreach my $transcript ( @{ $gene->get_all_Transcripts() } ) {
print "TRANSCRIPT ", $transcript->stable_id(), "\n";
print_DBEntries( $transcript->get_all_DBEntries() );
# Watch out: pseudogenes have no translation
if ( defined $transcript->translation() ) {
my $translation = $transcript->translation();
print "TRANSLATION ", $translation->stable_id(), "\n";
print_DBEntries( $translation->get_all_DBEntries() );
}
}
OUTPUT
======
$ perl dbentry_test.pl
GENE ENSG00000133103
Use of uninitialized value in printf at dbentry_test.pl line 15.
XREF OTTHUMG00000016768 ()
Use of uninitialized value in printf at dbentry_test.pl line 15.
XREF COG6 ()
TRANSCRIPT ENST00000416691
Can't locate object method "add_linkage_type" via package "Bio::EnsEMBL::Identit
yXref" at /cygdrive/c/Bioinformatics/Ensembl/src/ensembl/modules/Bio/EnsEMBL/DBS
QL/DBEntryAdaptor.pm line 1262.
Any ideas why this no longer works? Last time I ran this was with build 56.
Looks like $dbe->dbname() is undefined?
Dave Burt
--
The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
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