merge from vega-41-dev

modules/Bio/EnsEMBL/Utils/ConversionSupport.pm

@@ -1079,7 +1079,7 @@ sub split_chromosomes_by_size {
             push @{ $top_slices }, $slice_adaptor->fetch_by_region('chromosome', $chr);
         }
     } else {
-        $top_slices = $slice_adaptor->fetch_all("toplevel");
+        $top_slices = $slice_adaptor->fetch_all('chromosome');
     }
 
     my ($big_chr, $small_chr, $min_big_chr, $min_small_chr);

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

+package Bio::EnsEMBL::Utils::VegaCuration::Gene;
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Steve Trevanion <st3@sanger.ac.uk>
+
+=head1 CONTACT
+
+Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
+
+=cut
+
+use strict;
+use warnings;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Utils::ConversionSupport;
+
+@ISA = qw(Bio::EnsEMBL::Utils::ConversionSupport);
+
+
+=head2 find_gaps
+
+   Args       : arrayref of B::E::Transcripts
+   Example    : my $gaps = find_gaps($all_transcripts)
+   Description: identifies regions of a gene that are not covered by any transcript
+   Returntype : int
+   Exceptions : none
+   Caller     : internal
+
+=cut
+
+sub find_gaps {
+	my $self = shift;
+	my ($all_transcripts) = @_;
+	my $gaps = 0;
+	my @sorted_transcripts = sort {$a->start <=> $b->start || $b->end <=> $a->end} @{$all_transcripts};
+	my $first_transcript = shift @sorted_transcripts;
+	my $pos = $first_transcript->end;
+	foreach my $transcript (@sorted_transcripts) {
+		next if ($transcript->end < $pos );
+		if ($transcript->start < $pos && $transcript->end > $pos ) {
+			$pos = $transcript->end;			
+			next;
+		}
+		elsif ($transcript->end > $pos) {
+			$gaps++;
+			$pos = $transcript->end;
+		}
+	}
+	return $gaps;		
+}

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

+package Bio::EnsEMBL::Utils::VegaCuration::Transcript;
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Steve Trevanion <st3@sanger.ac.uk>
+
+=head1 CONTACT
+
+Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
+
+=cut
+
+use strict;
+use warnings;
+use vars qw(@ISA);
+
+use Bio::EnsEMBL::Utils::VegaCuration::Gene;
+
+@ISA = qw(Bio::EnsEMBL::Utils::VegaCuration::Gene);
+

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

+package Bio::EnsEMBL::Utils::VegaCuration::Translation;
+
+=head1 NAME
+
+=head1 SYNOPSIS
+
+=head1 DESCRIPTION
+
+=head1 LICENCE
+
+This code is distributed under an Apache style licence:
+Please see http://www.ensembl.org/code_licence.html for details
+
+=head1 AUTHOR
+
+Steve Trevanion <st3@sanger.ac.uk>
+
+=head1 CONTACT
+
+Post questions to the EnsEMBL development list ensembl-dev@ebi.ac.uk
+
+=cut
+
+use strict;
+use warnings;
+use vars qw(@ISA);
+
+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
+   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);
+
+	#hasref 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_1'} = 1;
+			}
+			else {
+				$results->{'END_MISSING_2'} = $stop_codon;
+			}
+		}
+	}
+
+
+	#extra CDS start not found remark
+	if (grep {$_->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_1'} = 1;
+			} else {
+				$results->{'START_MISSING_2'} = $start_codon;
+			}
+		}
+	}
+
+	return $results;
+}