Raw content of Bio::EnsEMBL::Utils::VegaCuration::Translation =head1 LICENSE Copyright (c) 1999-2009 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 /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 =head1 SYNOPSIS =head1 DESCRIPTION =head1 METHODS =cut package Bio::EnsEMBL::Utils::VegaCuration::Translation; use strict; use warnings; use vars qw(@ISA); use Data::Dumper; use Bio::EnsEMBL::Utils::VegaCuration::Transcript; @ISA = qw(Bio::EnsEMBL::Utils::VegaCuration::Transcript); =head2 check_CDS_end_remarks Args : B::E::Transcript Example : my $results = $support->check_CDS_end_remarks($transcript) Description: identifies incorrect 'CDS end...' transcript remarks in a otter-derived Vega database Returntype : hashref =cut sub check_CDS_start_end_remarks { my $self = shift; my $trans = shift; # info for checking my @remarks = @{$trans->get_all_Attributes('remark')}; my $coding_end = $trans->cdna_coding_end; my $coding_start = $trans->cdna_coding_start; my $trans_end = $trans->length; my $trans_seq = $trans->seq->seq; my $stop_codon = substr($trans_seq, $coding_end-3, 3); my $start_codon = substr($trans_seq, $coding_start-1, 3); #hashref to return results my $results; #extra CDS end not found remarks if (grep {$_->value eq 'CDS end not found'} @remarks) { if ( ($coding_end != $trans_end) && ( grep {$_ eq $stop_codon} qw(TGA TAA TAG) ) ) { $results->{'END_EXTRA'} = 1; } } #missing CDS end not found remark if ( $coding_end == $trans_end ) { if (! grep {$_->value eq 'CDS end not found'} @remarks) { if (grep {$_ eq $stop_codon} qw(TGA TAA TAG)) { $results->{'END_MISSING_2'} = 1; } else { $results->{'END_MISSING_1'} = $stop_codon; } } } #extra CDS start not found remark if (grep {$_->value eq 'CDS start not found'} @remarks) { if ( ($coding_start != 1) && ($start_codon eq 'ATG') ) { $results->{'START_EXTRA'} = 1; } } #missing CDS start not found remark if ( $coding_start == 1) { if ( ! grep {$_->value eq 'CDS start not found'} @remarks) { if ($start_codon eq 'ATG') { $results->{'START_MISSING_2'} = 1; } else { $results->{'START_MISSING_1'} = $start_codon; } } } return $results; } =head2 check_CDS_end_remarks_loutre Args : B::E::Transcript Example : my $results = $support->check_CDS_end_remarks($transcript) Description: identifies incorrect 'CDS end...' transcript attribs in a loutre of a loutre-derived Vega database. Returntype : hashref =cut sub check_CDS_start_end_remarks_loutre { my $self = shift; my $trans = shift; # info for checking my @stops = qw(TGA TAA TAG); my %attributes; foreach my $attribute (@{$trans->get_all_Attributes()}) { $attributes{$attribute->code} = $attribute; } my $coding_end = $trans->cdna_coding_end; my $coding_start = $trans->cdna_coding_start; my $trans_end = $trans->length; my $trans_seq = $trans->seq->seq; my $stop_codon = substr($trans_seq, $coding_end-3, 3); my $start_codon = substr($trans_seq, $coding_start-1, 3); #hashref to return results my $results; #extra CDS end not found remarks if ( ($attributes{'cds_end_NF'}->value == 1) && ($coding_end != $trans_end) && ( grep {$_ eq $stop_codon} @stops) ) { $results->{'END_EXTRA'} = 1; } #missing CDS end not found remark if ( $coding_end == $trans_end ) { if ($attributes{'cds_end_NF'}->value == 0 ) { if (grep {$_ eq $stop_codon} @stops) { $results->{'END_MISSING_2'} = 1; } else { $results->{'END_MISSING_1'} = $stop_codon; } } } #extra CDS start not found remark if ( ($attributes{'cds_start_NF'}->value == 1 ) && ($coding_start != 1) && ($start_codon eq 'ATG') ) { $results->{'START_EXTRA'} = 1; } #missing CDS start not found remark if ( $coding_start == 1) { if ( $attributes{'cds_start_NF'}->value == 0 ) { if ($start_codon eq 'ATG') { $results->{'START_MISSING_2'} = 1; } else { $results->{'START_MISSING_1'} = $start_codon; } } } return $results; } =head2 get_havana_seleno_comments Args : none Example : my $results = $support->get_havana_seleno_comments Description: parses the HEREDOC containing Havana comments in this module Returntype : hashref =cut sub get_havana_seleno_comments { my $seen_translations; while (<DATA>) { next if /^\s+$/ or /#+/; my ($obj,$comment) = split /=/; $obj =~ s/^\s+|\s+$//g; $comment =~ s/^\s+|\s+$//g; $seen_translations->{$obj} = $comment; } return $seen_translations; } sub check_for_stops { my $support = shift; my ($gene,$seen_transcripts) = @_; my $gname = $gene->get_all_Attributes('name')->[0]->value; my $scodon = 'TGA'; my $mod_date = $support->date_format( $gene->modified_date,'%d/%m/%y' ); 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_verbose("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) from gene $gname has non \'$scodon\' stop codons [$mod_date]:\nSequence = $orig_seq\nStops at $positions)\n\n"); } else { $support->log_warning("INTERNAL STOPS EXTERNAL: Transcript $tsi ($tname) from gene $gname has non \'$scodon\' stop codons[$mod_date]:\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 $tsi stored as Annotation_remark not hidden remark) [$mod_date]\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) [$mod_date]\n"); } # catch old annotations where number off by one elsif (($found_stops[$i]->[1]) == $offset+1) { $support->log_warning("PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]\n"); } else { $support->log_warning("Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]\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}.") [$mod_date]\n"); } else { $support->log("POTENTIAL SELENO ($seq) in $tsi ($tname, gene $gname) found at $pos [$mod_date]\n"); } } } } } } #details of annotators comments __DATA__ OTTHUMT00000144659 = FIXED- changed to transcript OTTHUMT00000276377 = FIXED- changed to transcript OTTHUMT00000257741 = FIXED- changed to nmd OTTHUMT00000155694 = NOT_FIXED- should be nmd but external annotation but cannot be fixed OTTHUMT00000155695 = NOT_FIXED- should be nmd but external annotation but cannot be fixed OTTHUMT00000282573 = FIXED- changed to unprocessed pseudogene OTTHUMT00000285227 = FIXED- changed start site OTTHUMT00000151008 = FIXED- incorrect trimming of CDS, removed extra stop codon OTTHUMT00000157999 = FIXED- changed incorrect stop OTTHUMT00000150523 = FIXED- incorrect trimming of CDS OTTHUMT00000150525 = FIXED- incorrect trimming of CDS OTTHUMT00000150522 = FIXED- incorrect trimming of CDS OTTHUMT00000150521 = FIXED- incorrect trimming of CDS OTTHUMT00000246819 = FIXED- corrected frame OTTHUMT00000314078 = FIXED- corrected frame OTTHUMT00000080133 = FIXED- corrected frame OTTHUMT00000286423 = FIXED- changed to transcript OTTMUST00000055509 = FIXED- error OTTMUST00000038729 = FIXED- corrected frame OTTMUST00000021760 = FIXED- corrected frame OTTMUST00000023057 = FIXED- corrected frame OTTMUST00000015207 = FIXED- corrected frame OTTMUST00000056646 = FIXED- error OTTMUST00000059686 = FIXED- corrected frame OTTMUST00000013426 = FIXED- corrected frame OTTMUST00000044412 = FIXED- error