Fetch all the transcript variant structure (in terms of exons) from a core

database in GFF format (STDOUT).

misc-scripts/alternative_splicing/Fetch_gff.pl

+#!/usr/local/ensembl/bin/perl -w
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2010 The European Bioinformatics Institute and
+  Genome Research Limited.  All rights reserved.
+
+  This software is distributed under a modified Apache license.
+  For license details, please see
+
+    http://www.ensembl.org/info/about/code_licence.html
+
+=head1 CONTACT
+
+  Please email comments or questions to the public Ensembl
+  developers list at <ensembl-dev@ebi.ac.uk>.
+
+  Questions may also be sent to the Ensembl help desk at
+  <helpdesk@ensembl.org>.
+
+=cut
+
+=head1 NAME
+
+ Fetch_gff.pl
+
+=head1 AUTHORS
+
+ Gautier Koscielny (koscieln@ebi.ac.uk)
+
+=head1 SYNOPSIS
+
+  Fetch_gff.pl -dbhost host -dbuser ensro -dbname homo_sapiens_core_57_37b
+
+=head1 DESCRIPTION
+
+This script generates a GFF file containing all the transcript variants 
+from an Ensembl core database.
+
+here is an example commandline
+
+  ./Fetch_gff.pl -dbhost host -dbuser user -dbname my_db -dbpass ****
+
+=head1 OPTIONS
+
+    -dbhost    host name for database (gets put as host= in locator)
+    -dbname    what name to connect to (dbname= in locator)
+    -dbuser    what username to connect as (dbuser= in locator)
+    -dbpass    what password to use (dbpass= in locator)
+    -chr       which chromosome (optional)
+    -help      displays this documentation with PERLDOC
+
+=cut
+
+use strict;
+use warnings;
+
+use Bio::EnsEMBL::Feature;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::Utils::Exception qw(throw);
+
+use POSIX qw(ceil);
+
+use Getopt::Long;
+use Bio::EnsEMBL::Utils::Exception qw(throw warning);
+
+{ # block to avoid namespace pollution
+  my $host   = '';
+  my $port   = '';
+  my $dbname = '';
+  my $dbuser = '';
+  my $dbpass = '';
+	my $chr    = undef;
+  my $help;
+  my @coord_system;
+
+  &GetOptions(
+              'dbhost:s'   => \$host,
+              'dbport:n'   => \$port,
+              'dbname:s'   => \$dbname,
+              'dbuser:s'   => \$dbuser,
+							'chr:s'      => \$chr,
+              'dbpass:s'   => \$dbpass,
+              'h|help'     => \$help,
+             ) or ($help = 1);
+
+  if(!$host || !$dbuser || !$dbname || !$dbpass){
+    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 @stable_gene_ids = undef;
+	my $size = 0;
+
+	if (defined($chr)) {
+
+			my $slice_adaptor = $db->get_SliceAdaptor();
+			my $slice = $slice_adaptor->fetch_by_region( 'chromosome', $chr );
+			@stable_gene_ids = @{ $gene_adaptor->fetch_all_by_Slice($slice) };
+			$size = scalar @stable_gene_ids;
+			print STDERR "Number of stable genes on region $chr:\t" . $size . "\n";
+
+	} else {
+
+			@stable_gene_ids = @{$gene_adaptor->list_stable_ids()};
+			$size = scalar @stable_gene_ids;
+			print STDERR "Number of stable ids:\t" . $size . "\n";
+	}
+
+	for my $id (@stable_gene_ids) {
+			
+			my $gene = ($chr) ? $id : $gene_adaptor->fetch_by_stable_id($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 = $gene->end();
+			
+			my @transcripts = @{$gene->get_all_Transcripts()};
+			for my $transcript (@transcripts) {
+					
+					my $transcr_id = $transcript->display_id() ; ;
+					
+					#Get the exons + print info.
+					my $exons = $transcript->get_all_Exons() ;
+					
+					foreach my $exon (@$exons) {
+							my $exon_id = $exon->display_id() ;
+							my $exon_start = $exon->start() ;
+							my $exon_end = $exon->end() ;
+							my $exon_std = $exon->strand() ;
+							my $slice = $exon->slice->seq_region_name();
+							$exon_std =~ s/-1/-/ ;
+							$exon_std =~ s/1/+/ ;
+							print "$chr\tEnsembl\texon\t$exon_start\t$exon_end\t.\t$exon_std\t.\tgene_id \"$gene_id\"; transcript_id \"$transcr_id\"; exon_id \"$exon_id\"\n" ;
+					}
+			}
+			
+	}
+	
+	exit 0;
+
+}