merge from vega-48-dev

modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm

@@ -186,6 +186,145 @@ sub get_havana_seleno_comments {
 	return $seen_translations;
 }
 
+sub check_for_stops {
+	my $support = shift;
+	my ($gene,$seen_transcripts) = @_;
+	my $scodon = 'TGA';
+
+ TRANS:
+	foreach my $trans (@{$gene->get_all_Transcripts}) {
+		my $tsi = $trans->stable_id;
+		my $tID = $trans->dbID;
+		my $tname = $trans->get_all_Attributes('name')->[0]->value;
+		$support->log_verbose("Studying transcript $tsi ($tname, $tID)\n",1);
+		
+		my $peptide;
+		
+		# go no further if the transcript doesn't translate or if there are no stops
+		next TRANS unless ($peptide = $trans->translate);
+
+		my $pseq = $peptide->seq;
+		my $orig_seq = $pseq;
+		
+		# (translate method trims stops from sequence end)
+		next TRANS unless ($pseq =~ /\*/);
+		$support->log("Stops found in $tsi ($tname)\n",1);
+		
+		# find out where and how many stops there are
+		my @found_stops;
+		my $mrna   = $trans->translateable_seq;
+		my $offset = 0;
+		my $tstop;
+		while ($pseq =~ /([^\*]+)\*(.*)/) {
+			my $pseq1_f = $1;
+			$pseq = $2;
+			my $seq_flag = 0;
+			$offset += length($pseq1_f) * 3;
+			my $stop = substr($mrna, $offset, 3);
+			my $aaoffset = int($offset / 3)+1;
+			push(@found_stops, [ $stop, $aaoffset ]);
+			$tstop .= "$aaoffset ";
+			$offset += 3;
+		}
+		
+		# are all stops TGA...?
+		my $num_stops = scalar(@found_stops);
+		my $num_tga = 0;
+		my $positions;
+		foreach my $stop (@found_stops) {
+			$positions .= $stop->[0]."(".$stop->[1].") ";
+			if ($stop->[0] eq $scodon) {
+				$num_tga++;
+			}
+		}
+		
+		my $source = $gene->source;
+		#...no - an internal stop codon error in the database...
+		if ($num_tga < $num_stops) {
+			if ($source eq 'havana') {
+				$support->log_warning("INTERNAL STOPS HAVANA: Transcript $tsi ($tname) has non \'$scodon\' stop codons:\nSequence = $orig_seq\nStops at $positions\n\n");
+			}
+			else {
+				$support->log_verbose("INTERNAL STOPS EXTERNAL: Transcript $tsi ($tname) has non \'$scodon\' stop codons:\nSequence = $orig_seq\nStops at $positions\n\n");
+			}
+			
+		}
+		#...yes - check remarks
+		else {
+			my $flag_remark  = 0; # 1 if word seleno has been used
+			my $flag_remark2 = 0; # 1 if existing remark has correct numbering
+			
+			my $alabel       = 'Annotation_remark- selenocysteine ';
+			my $alabel2      = 'selenocysteine ';
+			
+			my $annot_stops;
+			my $remarks;
+			
+			#get both hidden_remarks and remarks
+			foreach my $remark_type ('remark','hidden_remark') {
+				foreach my $attrib ( @{$trans->get_all_Attributes($remark_type)}) {
+					push @{$remarks->{$remark_type}}, $attrib->value;
+				}
+			}
+			
+			#parse remarks to check syntax for location of edits
+			while (my ($attrib,$remarks)= each %$remarks) {
+				foreach my $text (@{$remarks}) {					
+					if ( ($attrib eq 'remark') && ($text=~/^$alabel(.*)/) ){
+						$support->log_warning("seleno remark for $tsi stored as Annotation_remark not hidden remark\n");
+						$annot_stops=$1;
+					}
+					elsif ($text =~ /^$alabel2(.*)/) {
+						$annot_stops=$1;
+					}
+				}
+			}
+			
+			#check the location of the annotated edits matches actual stops in the sequence
+			my @annotated_stops;
+			if ($annot_stops){
+				my $i = 0;
+				foreach my $offset (split(/\s+/, $annot_stops)) {
+					# not a number - ignore
+					if ($offset!~/^\d+$/){
+					}
+					#OK if it matches a known stop
+					elsif ($found_stops[$i]->[1] == $offset) {
+						push  @annotated_stops, $offset;
+					}
+					# catch old annotations where number was in DNA not peptide coordinates
+					elsif (($found_stops[$i]->[1] * 3) == $offset) {
+						$support->log_warning("DNA: Annotated stop for transcript tsi ($tname) is in DNA not peptide coordinates\n");
+					}
+					# catch old annotations where number off by one
+					elsif (($found_stops[$i]->[1]) == $offset+1) {
+						$support->log_warning("PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one\n");
+					}
+					else {
+						$support->log_warning("Annotated stop for transcript $tsi ($tname) does not match a TGA codon\n");
+						push  @annotated_stops, $offset;
+				}						
+					$i++;
+				}
+			}
+			
+			#check location of found stops matches annotated ones - any new ones are reported
+			foreach my $stop ( @found_stops ) {
+				my $pos = $stop->[1];
+				my $seq = $stop->[0];
+				unless ( grep { $pos == $_} @annotated_stops) {
+					if ($seen_transcripts->{$tsi}) {
+						$support->log_verbose("Transcript $tsi ($tname) has potential selenocysteines but has been discounted by annotators:\n\t".$seen_transcripts->{$tsi}."\n");
+					}
+					else {
+						$support->log("POTENTIAL SELENO ($seq) in $tsi ($tname) found at $pos\n");
+					}
+				}
+			}
+		}
+	}
+}
+
 
 #details of annotators comments
 __DATA__