*** empty log message ***

misc-scripts/anopheles_scripts/check_stops.pl

+#!/usr/local/bin/perl
+
+=head1 NAME
+
+  dump_translations.pl
+
+=head1 SYNOPSIS
+ 
+  dump_translations.pl
+
+=head1 DESCRIPTION
+
+dump_translations.pl dumps out the translations of all the genes in a database specified in GeneConf.pm
+It\'s a stripped down version of gene2flat.
+
+=head1 OPTIONS
+
+=cut
+
+use strict;
+
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::SeqIO;
+use Bio::EnsEMBL::DBSQL::ProteinAdaptor;
+
+my $host = 'ecs2d';
+my $dbuser = 'ensro';
+my $dbname = 'homo_sapiens_core_10_30';
+my $dbpass;
+my $path;
+my $port;
+
+
+my $type = 'ensembl';
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(
+					    '-host'   => $host,
+					    '-user'   => $dbuser,
+					    '-dbname' => $dbname,
+					    '-pass'   => $dbpass,
+					    '-port'   => $port
+					    );
+
+
+print STDERR "Connecting to $host, $dbname\n";
+
+#my $query = "select t.transcript_id,t.translation_id from transcript t, gene g where t.gene_id = g.gene_id and g.type = '$type'"; 
+#my $sth = $db->prepare($query);
+#$sth->execute();
+
+my $gene_adaptor = $db->get_GeneAdaptor;
+
+my $gene_id_list = $gene_adaptor->list_geneIds;
+
+
+
+while(my $gene_id = shift(@$gene_id_list)) {
+    
+    #my ($transc_dbid, $transl_dbid) = @array;
+    
+    my $gene = $gene_adaptor->fetch_by_dbID($gene_id,1);
+    
+    foreach my $tr(@{$gene->get_all_Transcripts}) { 
+	
+	my $spl_sq = $tr->spliced_seq;
+	my $c_start = $tr->cdna_coding_start;
+	my $c_end = $tr->cdna_coding_end;
+	
+	my $pep = $tr->translate->seq;
+	
+	print STDERR $tr->stable_id()," ";
+	if ($pep =~ /\*$/) {
+	    print STDERR "STOP CODON INCLUDED\n";
+	}
+	
+	else {
+	    if ($c_end < length($spl_sq)) {
+		print STDERR "UTR - ";
+		my $codon = substr($spl_sq,$c_end,3);
+		if ($codon =~ /TAG|TGA|TAA/i) {
+		    print STDERR "STOP AFTER TRANSCRIPT\n";
+		}
+		else {
+		    print STDERR "NOSTOP AFTER TRANSCRIPT\n";
+		}
+	    }
+	    else {
+		print STDERR "NO UTR - ";
+		my $end_exon = $tr->end_Exon;
+		my $strand = $end_exon->strand;
+		my $last_codon;
+		if ($strand == 1) {
+		    $last_codon = $end_exon->contig->subseq($end_exon->end+1,$end_exon->end+3,1);
+		}
+		
+		else {
+		    $last_codon = $end_exon->contig->subseq($end_exon->start-3,$end_exon->start-1,-1);
+		}
+		
+		if ($last_codon =~ /TAG|TGA|TAA/i) {
+		    print STDERR "STOP AFTER TRANSCRIPT\n";
+		}
+		else {
+		    print STDERR "NOSTOP AFTER TRANSCRIPT\n";
+		}
+		
+	    }
+	    
+	}
+    }
+
+}
+
+
+
+