diff --git a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
index 2c864f5f0a4d76dfb0e7e8cec546eb67ff7d0305..554a736456499671e6bb3fa464afb19a3ee7e093 100644
--- a/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
+++ b/modules/Bio/EnsEMBL/Utils/VegaCuration/Translation.pm
@@ -201,12 +201,12 @@ sub check_for_stops {
foreach my $rem (@$hidden_remak_ttributes) {
if ($rem->value =~ /not_for_Vega/) {
#$support->log_verbose("Skipping transcript $tname ($tsi) since 'not_for_Vega'\n",1);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Skipping transcript $tname ($tsi) since 'not_for_Vega'\n");
+ $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Skipping transcript $tname ($tsi) since 'not_for_Vega'");
next TRANS;
}
}
#$support->log_verbose("Studying transcript $tsi ($tname, $tID)\n",1);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Studying transcript $tsi ($tname, $tID)\n");
+ $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Studying transcript $tsi ($tname, $tID)");
my $peptide;
# go no further if the transcript doesn't translate or if there are no stops
@@ -216,7 +216,7 @@ sub check_for_stops {
# (translate method trims stops from sequence end)
next TRANS unless ($pseq =~ /\*/);
#$support->log_verbose("Stops found in $tsi ($tname)\n",1);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Stops found in $tsi ($tname)\n");
+ $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Stops found in $tsi ($tname)");
# find out where and how many stops there are
my @found_stops;
@@ -331,7 +331,7 @@ sub check_for_stops {
#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".$seen_transcripts->{$tsi}.") [$mod_date]\n");
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, 'VQCT_pot_selC', "Transcript $tsi ($tname) has potential selenocysteines but has been discounted by annotators:\n".$seen_transcripts->{$tsi}.") [$mod_date]");
+ $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, 'VQCT_pot_selC', "Transcript $tsi ($tname) has potential selenocysteines but has been discounted by annotators: ".$seen_transcripts->{$tsi}.") [$mod_date]");
}
else {
#$support->log("POTENTIAL SELENO ($seq) in $tsi ($tname, gene $gname) found at $pos [$mod_date]\n");
@@ -380,370 +380,4 @@ OTTMUST00000015207 = FIXED- corrected frame
OTTMUST00000056646 = FIXED- error
OTTMUST00000059686 = FIXED- corrected frame
OTTMUST00000013426 = FIXED- corrected frame
-OTTMUST00000044412 = FIXED- error
-=======
-=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 <dev@ensembl.org>.
- 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;
- }
-# warn $trans->stable_id;
-# warn Data::Dumper::Dumper(\%attributes);
- 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_offset = 3 + $trans->translation->end_Exon->end_phase;
- 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'}) {
- if ( ($attributes{'cds_end_NF'}->value == 1)
- && ($coding_end != $trans_end)
- && ( grep {$_ eq $stop_codon} @stops) ) {
-# warn $trans->stable_id.": $coding_end--$trans_end--$stop_codon";
-# warn $trans->translation->end_Exon->end_phase;
- $results->{'END_EXTRA'} = $stop_codon;
- }
- }
- #missing CDS end not found remark
- if ( $coding_end == $trans_end ) {
- if ($attributes{'cds_end_NF'}) {
- if ($attributes{'cds_end_NF'}->value == 0 ) {
- if (! grep {$_ eq $stop_codon} @stops) {
-# warn $trans->stable_id.": $coding_end--$trans_end--$stop_codon";
-# warn $trans->translation->end_Exon->end_phase;
- $results->{'END_MISSING'}{'WRONG'} = $stop_codon;
- }
- }
- }
- elsif (! grep {$_ eq $stop_codon} @stops) {
- $results->{'END_MISSING'}{'ABSENT'} = $stop_codon;
- }
- }
- #extra CDS start not found remark
- if ( $attributes{'cds_start_NF'}) {
- if ( ($attributes{'cds_start_NF'}->value == 1 )
- && ($start_codon eq 'ATG') ) {
- $results->{'START_EXTRA'} = $start_codon;
- }
- }
- #missing CDS start not found remark
- if ( $coding_start == 1) {
- if ( $attributes{'cds_start_NF'} ) {
- if ( $attributes{'cds_start_NF'}->value == 0 ) {
- if ($start_codon ne 'ATG') {
- $results->{'START_MISSING'}{'WRONG'} = $start_codon;
- }
- }
- }
- elsif ($start_codon ne 'ATG') {
- $results->{'START_MISSING'}{'ABSENT'} = $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,$seen_transcripts,$log_object) = @_;
- if(not defined $log_object){
- $log_object=$support;
- }
-
- my $gname = $gene->get_all_Attributes('name')->[0]->value;
- my $gsi = $gene->stable_id;
- 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;
- foreach my $rem (@{$trans->get_all_Attributes('hidden_remark')}) {
- if ($rem->value =~ /not_for_Vega/) {
- #$support->log_verbose("Skipping transcript $tname ($tsi) since 'not_for_Vega'\n",1);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Skipping transcript $tname ($tsi) since 'not_for_Vega'\n");
- next TRANS;
- }
- }
- #$support->log_verbose("Studying transcript $tsi ($tname, $tID)\n",1);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Studying transcript $tsi ($tname, $tID)\n");
- 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);
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, '', "Stops found in $tsi ($tname)\n");
-
- # 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");
- $log_object->_save_log('log_warning', '', $gsi, 'TRANSCRIPT', $tsi, 'VQCT_internal_stop', "INTERNAL STOPS HAVANA: Transcript $tsi ($tname) from gene $gname has non \'$scodon\' stop codons [$mod_date]: Sequence = $orig_seq Stops at $positions)");
- }
- else {
- #$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");
- $log_object->_save_log('log_warning', '', $gsi, 'TRANSCRIPT', $tsi, 'VQCT_internal_stop', "INTERNAL STOPS EXTERNAL: Transcript $tsi ($tname) from gene $gname has non \'$scodon\' stop codons[$mod_date]: Sequence = $orig_seq Stops at $positions)");
- }
- }
- #...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");
- $log_object->_save_log('log_warning', '', $gsi, '', $tsi, 'VQCT_wrong_selC_coord', "seleno remark for $tsi stored as Annotation_remark not hidden remark) [$mod_date]");
- $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;
- my $defined_offset=0;
- my $defined_found_stop=0;
- foreach my $offset (split(/\s+/, $annot_stops)) {
- $defined_offset= (defined($offset)) && ($offset=~/^\d+$/);
- $defined_found_stop = ( defined(@found_stops) && defined($found_stops[$i]) && defined($found_stops[$i]->[1]));
- # not a number - ignore
- #OK if it matches a known stop
- if ($defined_offset && $defined_found_stop && ($found_stops[$i]->[1] == $offset)) {
- push @annotated_stops, $offset;
- }
- # catch old annotations where number was in DNA not peptide coordinates
- elsif ($defined_offset && $defined_found_stop && (($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");
- $log_object->_save_log('log_warning', '', $gsi, 'DNA', $tsi, 'VQCT_wrong_selC_coord', "DNA: Annotated stop for transcript tsi ($tname) is in DNA not peptide coordinates) [$mod_date]");
- }
- # catch old annotations where number off by one
- elsif ($defined_offset && $defined_found_stop && (($found_stops[$i]->[1]) == $offset+1)) {
- #$support->log_warning("PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]\n");
- $log_object->_save_log('log_warning', '', $gsi, 'PEPTIDE', $tsi, 'VQCT_wrong_selC_coord', "PEPTIDE: Annotated stop for transcript $tsi ($tname) is out by one) [$mod_date]");
- }
- elsif($defined_offset) {
- #$support->log_warning("Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]\n");
- $log_object->_save_log('log_warning', '', $gsi, 'TRANSCRIPT', $tsi, 'VQCT_wrong_selC_coord', "Annotated stop for transcript $tsi ($tname) does not match a TGA codon) [$mod_date]");
- 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 = $stop->[0];
- if(!(defined($pos) && defined($_) && ( grep { $pos == $_} @annotated_stops))){
- #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".$seen_transcripts->{$tsi}.") [$mod_date]\n");
- $log_object->_save_log('log_verbose', '', $gsi, '', $tsi, 'VQCT_pot_selC', "Transcript $tsi ($tname) has potential selenocysteines but has been discounted by annotators:\n".$seen_transcripts->{$tsi}.") [$mod_date]");
- }
- else {
- #$support->log("POTENTIAL SELENO ($seq) in $tsi ($tname, gene $gname) found at $pos [$mod_date]\n");
- $log_object->_save_log('log', '', $gsi, '', $tsi, 'VQCT_pot_selC', "POTENTIAL SELENO ($seq) in $tsi ($tname, gene $gname) found at $pos [$mod_date]");
- }
- }
- }
- }
- }
-}
-sub _save_log{
- my $self=shift;
- my $log_type = shift;
- my $chrom_name=shift || '';
- my $gsi=shift || '';
- my $type=shift || '';
- my $tsi=shift || '';
- my $tag=shift || '';
- my $txt=shift || '';
- $self->$log_type($txt);
-}
-#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
+OTTMUST00000044412 = FIXED- error
\ No newline at end of file