[ensembl-dev] MXEs labeling the pairs of transcripts (SOS) - With incomplete code.

[Andy Yates]

Dear Julio,

The SplicingEventAdaptor has a number of methods available for you to find events of your specified type. The following is untested code but should work:

my $slice = $db->get_SliceAdaptor()->fetch_by_region('toplevel', '1');
my $splicing_events = $se_adaptor->fetch_all_by_Slice($slice, 'MXE');

Getting all the events is now a case of iterating through all available toplevel sequence regions in the API. You should look at the SliceAdaptor documentation & the method fetch_all().

All the best,

Andy

Andrew Yates                   Ensembl Core Software Project Leader
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensembl.org/

On 18 Apr 2012, at 23:33, Julio wrote:

> Dear people-at-Ensembl, I hope you can help me with this: 
> 
> I need to filter the alternative splicing data for mutually exclusive exons labeling the pairs of transcripts that are involved in event. 
> 
> Thanks in advance! 
> 
> Best regards, Julio.
>   
> ###
> 
> 
> This code is incomplete and I am trying to finish it (I copied from http://lists.ensembl.org/pipermail/dev/2011-May/001226.html ).
> 
> #!/usr/local/ensembl/bin/perl -w
> 
> use lib "/home/julio/src/ensembl/modules"; 
> use strict;
> use warnings;
> use Getopt::Long;
> use Bio::EnsEMBL::Utils::Exception qw(throw warning);
> use Bio::EnsEMBL::Feature;
> use Bio::EnsEMBL::DBSQL::DBAdaptor;
> use Bio::EnsEMBL::DBSQL::SplicingEventAdaptor;
> use Bio::EnsEMBL::DBSQL::GeneAdaptor;
> use Bio::EnsEMBL::DBSQL::AttributeAdaptor;
> use Bio::EnsEMBL::DBSQL::SplicingTranscriptPairAdaptor;
> use Bio::EnsEMBL::Utils::Exception qw(throw);
> 
> my $host   = '';
> my $port   = '3306';
> my $dbname = '';
> my $dbuser = '';
> my $dbpass = '';
> my $file   = undef;
> my $help;
> my @coord_system;
> 
> &GetOptions(
>         'dbhost:s'   => \$host,
>         'dbport:n'   => \$port,
>         'dbname:s'   => \$dbname,
>         'dbuser:s'   => \$dbuser,
>         'file:s'      => \$file,
>         'dbpass:s'   => \$dbpass,
>         'h|help'     => \$help,
>         ) or ($help = 1);
> 
> if(!$host || !$dbuser || !$dbname) { 
>         print STDERR "Can't get any information without database details\n";
>         print STDERR "-dbhost $host -dbuser $dbuser -dbname $dbname ".
>                 " -dbpass $dbpass\n";
>         $help = 1;
> }
> 
> if ($help) {
>         exec('perldoc', $0);
> }
> 
> my $db = Bio::EnsEMBL::DBSQL::DBAdaptor->new
>         (-dbname => $dbname,
>          -host   => $host,
>          -user   => $dbuser,
>          -port   => $port,
>          -pass   => $dbpass);
> 
> my $gene_adaptor = $db->get_GeneAdaptor();
> my $se_adaptor = $db->get_SplicingEventAdaptor();
> my $attrib_adaptor = $db->get_AttributeAdaptor();
> my $SplicingTranscriptPairAdaptor = $db->get_SplicingTranscriptPairAdaptor();
> my @stable_gene_ids = @{$gene_adaptor->list_stable_ids()};
> my $size = scalar @stable_gene_ids;
> print STDERR "Number of stable ids:\t" . $size . "\n";
> 
> my $count = 0;
> 
> # example genes 
> my @genes = ("ENSG00000002016", "ENSG00000002746");
> 
> # don't know how to get this information easyly from the core API
> 
> my $attrib_names = {
>         MXE => "Mutually exclusive exons",    
>         };
> 
> print  " AS name\tType\tShort desc\tlocation\tdetails\n";
> print  "+--------------------------------------------------------------------------+\n";
> 
> for my $id (@genes) {
>         
>         $count++;
>         my $gene = $gene_adaptor->fetch_by_stable_id($id);    
>         my $gene_id = $gene->display_id();
>         my $biotype = $gene->biotype();
>         my $chr = $gene->slice->seq_region_name();
>         my $strand = $gene->strand();
>         my $start = $gene->start();
>         my $end = $gene->end();
>         
> #And get all the AS events sorted by type and location for a given gene:
>         
>         for my $se (  @ { $se_adaptor->fetch_all_by_Gene($gene) } ) {
>             
>             # filter on Mutually exclusive events
>             next unless ($se->type() eq 'MXE');
>             
>             # print location
>             my $location = ($se->strand() == 1) ? ("+\t$chr:" . $se->start() . "-" . $se->end()) : ("-\t$chr:" . $se->end() . "-" . $se->start());
>             print  $se->type() .  "\t$location";
>             
>          
>             # retrieve the trans
>             my $f = $f_map{$splicing_transcript_pair_id};
>             my $trans = $SplicingTranscriptPairAdaptor->fetch_by_dbID($splicing_transcript_pair_id);
>             
>             # concatenate information about this trans
> 
> 
>             # depending to which transcript the mutually exclusive exon is part of, assign this information to list s1 or s2
>                 
> 
>             # finally print this information
>             print "\tAlternative trans: " . join("; ", @s1) . " / " . join(";", @s2) . "\n";
>         }        
> }
> exit 0;
> 
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