From ac77391be76126beccc1ea3481befb953480a569 Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Sun, 1 Apr 2012 22:04:08 +0000
Subject: [PATCH] Replacing the 6 coordinate methods with versions which can
operate on transcripts which have not been persisted to a database. The DBID
is still used for caching purposes
---
modules/Bio/EnsEMBL/Exon.pm | 512 ++++++++++++++++++------------------
1 file changed, 252 insertions(+), 260 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 3266b535bd..6d34bcf321 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -398,33 +398,32 @@ sub strand {
=cut
sub cdna_start {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{cdna_start}->{$id}) {
+ return $self->{cdna_start}->{$id};
}
-
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'cdna_start'}->{$transcript_id} ) ) {
- my @coords =
- $transcript->genomic2cdna( $self->start(), $self->end(),
- $self->strand() );
-
- if ( @coords && !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap') ) {
- $self->{'cdna_start'}->{$transcript_id} = $coords[0]->start();
- } elsif (@coords) {
- throw("First part of exon maps into a gap");
- } else {
- throw("Can not map exon");
- }
+
+ my $cdna_start;
+ my @coords = $transcript->genomic2cdna($self->start(), $self->end(), $self->strand());
+ if(@coords && !$coords[0]->isa('Bio::EnsEMBL::Mapper::Gap')) {
+ $cdna_start = $coords[0]->start();
+ }
+ elsif(@coords) {
+ throw "Last part of exon maps into gap";
+ }
+ else {
+ throw "Can not map exon";
+ }
+
+ if(defined $id) {
+ $self->{cdna_start}->{$id} = $cdna_start;
}
- return $self->{'cdna_start'}->{$transcript_id};
+ return $cdna_start;
} ## end sub cdna_start
=head2 cdna_end
@@ -448,33 +447,32 @@ sub cdna_start {
=cut
sub cdna_end {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{cdna_end}->{$id}) {
+ return $self->{cdna_end}->{$id};
}
-
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'cdna_end'}->{$transcript_id} ) ) {
- my @coords =
- $transcript->genomic2cdna( $self->start(), $self->end(),
- $self->strand() );
-
- if ( @coords && !$coords[-1]->isa('Bio::EnsEMBL::Mapper::Gap') ) {
- $self->{'cdna_end'}->{$transcript_id} = $coords[-1]->end();
- } elsif (@coords) {
- throw("Last part of exon maps into gap");
- } else {
- throw("Can not map exon");
- }
+
+ my $cdna_end;
+ my @coords = $transcript->genomic2cdna($self->start(), $self->end(), $self->strand());
+ if(@coords && !$coords[-1]->isa('Bio::EnsEMBL::Mapper::Gap')) {
+ $cdna_end = $coords[-1]->end();
+ }
+ elsif(@coords) {
+ throw "Last part of exon maps into gap";
+ }
+ else {
+ throw "Can not map exon";
+ }
+
+ if(defined $id) {
+ $self->{cdna_end}->{$id} = $cdna_end;
}
- return $self->{'cdna_end'}->{$transcript_id};
+ return $cdna_end;
} ## end sub cdna_end
=head2 cdna_coding_start
@@ -497,56 +495,55 @@ sub cdna_end {
=cut
sub cdna_coding_start {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{cdna_coding_start}->{$id}) {
+ return $self->{cdna_coding_start}->{$id};
}
+
+ my $cdna_coding_start;
+ my $transcript_coding_start = $transcript->cdna_coding_start();
+ if(defined $transcript_coding_start) {
+ my $cdna_start = $self->cdna_start($transcript);
+
+ if ( $transcript_coding_start < $cdna_start ) {
+ # Coding region starts upstream of this exon...
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'cdna_coding_start'}->{$transcript_id} ) ) {
- my $transcript_coding_start = $transcript->cdna_coding_start();
-
- if ( !defined($transcript_coding_start) ) {
- # This is a non-coding transcript.
- $self->{'cdna_coding_start'}->{$transcript_id} = undef;
- $self->{'cdna_coding_end'}->{$transcript_id} = undef;
+ if ( $transcript->cdna_coding_end() < $cdna_start ) {
+ # ... and also ends upstream of this exon.
+ $cdna_coding_start = undef;
+ }
+ else {
+ # ... and does not end upstream of this exon.
+ $cdna_coding_start = $cdna_start;
+ }
} else {
- my $cdna_start = $self->cdna_start($transcript);
+ # Coding region starts either within or downstream of this
+ # exon.
- if ( $transcript_coding_start < $cdna_start ) {
- # Coding region starts upstream of this exon...
-
- if ( $transcript->cdna_coding_end() < $cdna_start ) {
- # ... and also ends upstream of this exon.
- $self->{'cdna_coding_start'}->{$transcript_id} = undef;
- } else {
- # ... and does not end upstream of this exon.
- $self->{'cdna_coding_start'}->{$transcript_id} = $cdna_start;
- }
- } else {
- # Coding region starts either within or downstream of this
- # exon.
-
- if ( $transcript_coding_start <= $self->cdna_end($transcript) )
- {
- # Coding region starts within this exon.
- $self->{'cdna_coding_start'}->{$transcript_id} =
- $transcript_coding_start;
- } else {
- # Coding region starts downstream of this exon.
- $self->{'cdna_coding_start'}->{$transcript_id} = undef;
- }
+ if ( $transcript_coding_start <= $self->cdna_end($transcript) ) {
+ # Coding region starts within this exon.
+ $cdna_coding_start = $transcript_coding_start;
}
- } ## end else [ if ( !defined($transcript_coding_start...
- } ## end if ( !exists( $self->{...
-
- return $self->{'cdna_coding_start'}->{$transcript_id};
+ else {
+ # Coding region starts downstream of this exon.
+ $cdna_coding_start = undef;
+ }
+ }
+ }
+ else {
+ $cdna_coding_start = undef;
+ }
+
+ if(defined $id) {
+ $self->{cdna_coding_start}->{$id} = $cdna_coding_start;
+ $self->{cdna_coding_end}->{$id} = undef if ! defined $cdna_coding_start;
+ }
+
+ return $cdna_coding_start;
} ## end sub cdna_coding_start
=head2 cdna_coding_end
@@ -569,56 +566,56 @@ sub cdna_coding_start {
=cut
sub cdna_coding_end {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{cdna_coding_end}->{$id}) {
+ return $self->{cdna_coding_end}->{$id};
}
-
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'cdna_coding_end'}->{$transcript_id} ) ) {
- my $transcript_coding_end = $transcript->cdna_coding_end();
-
- if ( !defined($transcript_coding_end) ) {
- # This is a non-coding transcript.
- $self->{'cdna_coding_start'}->{$transcript_id} = undef;
- $self->{'cdna_coding_end'}->{$transcript_id} = undef;
- } else {
- my $cdna_end = $self->cdna_end($transcript);
-
- if ( $transcript_coding_end > $cdna_end ) {
- # Coding region ends downstream of this exon...
-
- if ( $transcript->cdna_coding_start() > $cdna_end ) {
- # ... and also starts downstream of this exon.
- $self->{'cdna_coding_end'}->{$transcript_id} = undef;
- } else {
- # ... and does not start downstream of this exon.
- $self->{'cdna_coding_end'}->{$transcript_id} = $cdna_end;
- }
- } else {
- # Coding region ends either within or upstream of this
- # exon.
-
- if ( $transcript_coding_end >= $self->cdna_start($transcript) )
- {
- # Coding region ends within this exon.
- $self->{'cdna_coding_end'}->{$transcript_id} =
- $transcript_coding_end;
- } else {
- # Coding region ends upstream of this exon.
- $self->{'cdna_coding_end'}->{$transcript_id} = undef;
- }
+
+ my $cdna_coding_end;
+ my $transcript_coding_end = $transcript->cdna_coding_end();
+ if(defined $transcript_coding_end) {
+ my $cdna_end = $self->cdna_end($transcript);
+
+ if ( $transcript_coding_end > $cdna_end ) {
+
+ # Coding region ends downstream of this exon...
+ if ( $transcript->cdna_coding_start() > $cdna_end ) {
+ # ... and also starts downstream of this exon.
+ $cdna_coding_end = undef;
+ }
+ else {
+ # ... and does not start downstream of this exon.
+ $cdna_coding_end = $cdna_end;
}
- } ## end else [ if ( !defined($transcript_coding_end...
- } ## end if ( !exists( $self->{...
-
- return $self->{'cdna_coding_end'}->{$transcript_id};
+ }
+ else {
+ # Coding region ends either within or upstream of this
+ # exon.
+
+ if ( $transcript_coding_end >= $self->cdna_start($transcript) ) {
+ # Coding region ends within this exon.
+ $cdna_coding_end = $transcript_coding_end;
+ }
+ else {
+ # Coding region ends upstream of this exon.
+ $cdna_coding_end = undef;
+ }
+ }
+ }
+ else {
+ $cdna_coding_end = undef;
+ }
+
+ if(defined $id) {
+ $self->{cdna_coding_end}->{$id} = $cdna_coding_end;
+ $self->{cdna_coding_start}->{$id} = undef if ! defined $cdna_coding_end;
+ }
+
+ return $cdna_coding_end;
} ## end sub cdna_coding_end
=head2 coding_region_start
@@ -644,57 +641,56 @@ sub cdna_coding_end {
# of cdna_coding_start().
sub coding_region_start {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{coding_region_start}->{$id}) {
+ return $self->{coding_region_start}->{$id};
}
-
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'coding_region_start'}->{$transcript_id} ) ) {
- my $transcript_coding_start = $transcript->coding_region_start();
-
- if ( !defined($transcript_coding_start) ) {
- # This is a non-coding transcript.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- } else {
- my $start = $self->start();
-
- if ( $transcript_coding_start < $start ) {
- # Coding region starts upstream of this exon...
-
- if ( $transcript->coding_region_end() < $start ) {
- # ... and also ends upstream of this exon.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- } else {
- # ... and does not end upstream of this exon.
- $self->{'coding_region_start'}->{$transcript_id} = $start;
- }
- } else {
- # Coding region starts either within or downstream of this
- # exon.
-
- if ( $transcript_coding_start <= $self->end() ) {
- # Coding region starts within this exon.
- $self->{'coding_region_start'}->{$transcript_id} =
- $transcript_coding_start;
- } else {
- # Coding region starts downstream of this exon.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- }
+
+ my $coding_region_start;
+ my $transcript_coding_start = $transcript->cdna_coding_start();
+ if(defined $transcript_coding_start) {
+ my $start = $self->start();
+
+ if ( $transcript_coding_start < $start ) {
+ # Coding region starts upstream of this exon...
+
+ if ( $transcript->coding_region_end() < $start ) {
+ # ... and also ends upstream of this exon.
+ $coding_region_start = undef;
+ }
+ else {
+ # ... and does not end upstream of this exon.
+ $coding_region_start = $start;
}
- } ## end else [ if ( !defined($transcript_coding_start...
- } ## end if ( !exists( $self->{...
-
- return $self->{'coding_region_start'}->{$transcript_id};
+ }
+ else {
+ # Coding region starts either within or downstream of this
+ # exon.
+
+ if ( $transcript_coding_start <= $self->end() ) {
+ # Coding region starts within this exon.
+ $coding_region_start = $transcript_coding_start;
+ }
+ else {
+ # Coding region starts downstream of this exon.
+ $coding_region_start = undef;
+ }
+ }
+ }
+ else {
+ $coding_region_start = undef;
+ }
+
+ if(defined $id) {
+ $self->{coding_region_start}->{$id} = $coding_region_start;
+ $self->{coding_region_end}->{$id} = undef if ! defined $coding_region_start;
+ }
+
+ return $coding_region_start;
} ## end sub coding_region_start
=head2 coding_region_end
@@ -720,57 +716,54 @@ sub coding_region_start {
# of cdna_coding_end().
sub coding_region_end {
- my $self = shift;
- my ($transcript) = @_;
+ my ($self, $transcript) = @_;
+ assert_ref($transcript, 'Bio::EnsEMBL::Transcript', 'transcript');
- if ( !defined($transcript)
- || !ref($transcript)
- || !$transcript->isa('Bio::EnsEMBL::Transcript') )
- {
- throw("Argument is not a transcript");
+ my $id = $transcript->dbID();
+
+ if(defined $id && exists $self->{coding_region_end}->{$id}) {
+ return $self->{coding_region_end}->{$id};
}
-
- my $transcript_id = $transcript->dbID();
-
- if ( !exists( $self->{'coding_region_end'}->{$transcript_id} ) ) {
- my $transcript_coding_end = $transcript->coding_region_end();
-
- if ( !defined($transcript_coding_end) ) {
- # This is a non-coding transcript.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- } else {
- my $end = $self->end();
-
- if ( $transcript_coding_end > $end ) {
- # Coding region ends downstream of this exon...
-
- if ( $transcript->coding_region_start() > $end ) {
- # ... and also starts downstream of this exon.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- } else {
- # ... and does not start downstream of this exon.
- $self->{'coding_region_end'}->{$transcript_id} = $end;
- }
- } else {
- # Coding region ends either within or upstream of this
- # exon.
-
- if ( $transcript_coding_end >= $self->start() ) {
- # Coding region ends within this exon.
- $self->{'coding_region_end'}->{$transcript_id} =
- $transcript_coding_end;
- } else {
- # Coding region ends upstream of this exon.
- $self->{'coding_region_start'}->{$transcript_id} = undef;
- $self->{'coding_region_end'}->{$transcript_id} = undef;
- }
+
+ my $coding_region_end;
+ my $transcript_coding_end = $transcript->coding_region_end();
+ if(defined $transcript_coding_end) {
+
+ my $end = $self->end();
+ if($transcript_coding_end > $end) {
+ # Coding region ends downstream of this exon...
+
+ if ( $transcript->coding_region_start() > $end ) {
+ # ... and also starts downstream of this exon.
+ $coding_region_end = undef;
+ }
+ else {
+ # ... and does not start downstream of this exon.
+ $coding_region_end = $end;
}
- } ## end else [ if ( !defined($transcript_coding_end...
- } ## end if ( !exists( $self->{...
-
- return $self->{'coding_region_end'}->{$transcript_id};
+ }
+ else {
+ # Coding region ends either within or upstream of this
+ # exon.
+ if ( $transcript_coding_end >= $self->start() ) {
+ $coding_region_end = $transcript_coding_end;
+ }
+ else {
+ $coding_region_end = undef;
+ }
+ }
+ }
+ else {
+ # This is a non-coding transcript.
+ $coding_region_end = undef;
+ }
+
+ if(defined $id) {
+ $self->{coding_region_end}->{$id} = $coding_region_end;
+ $self->{coding_region_start}->{$id} = undef if ! defined $coding_region_end;
+ }
+
+ return $coding_region_end;
} ## end sub coding_region_end
=head2 slice
@@ -926,8 +919,8 @@ sub transform {
# catch for old style transform calls
if( !@_ || ( ref $_[0] &&
- ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" ))
- )) {
+ ($_[0]->isa( "Bio::EnsEMBL::Slice" ) or $_[0]->isa( "Bio::EnsEMBL::LRGSlice" ))
+ )) {
deprecate('Calling transform without a coord system name is deprecated.');
return $self->_deprecated_transform(@_);
}
@@ -1025,7 +1018,7 @@ sub add_supporting_features {
}
if ((defined $self->slice() && defined $feature->slice())&&
- ( $self->slice()->name() ne $feature->slice()->name())){
+ ( $self->slice()->name() ne $feature->slice()->name())){
throw("Supporting feat not in same coord system as exon\n" .
"exon is attached to [".$self->slice()->name()."]\n" .
"feat is attached to [".$feature->slice()->name()."]");
@@ -1034,8 +1027,8 @@ sub add_supporting_features {
foreach my $added_feature ( @{ $self->{_supporting_evidence} } ){
# compare objects
if ( $feature == $added_feature ){
- # this feature has already been added
- next FEATURE;
+ # this feature has already been added
+ next FEATURE;
}
}
@@ -1128,9 +1121,9 @@ sub find_supporting_evidence {
}
else {
if ($f->entire_seq()->name eq $self->slice()->name) {
- if ($f->end >= $self->start && $f->start <= $self->end && $f->strand == $self->strand) {
- $self->add_supporting_features($f);
- }
+ if ($f->end >= $self->start && $f->start <= $self->end && $f->strand == $self->strand) {
+ $self->add_supporting_features($f);
+ }
}
}
}
@@ -1344,8 +1337,8 @@ sub peptide {
else {
my ($e_id, $tr_id) = ($self->stable_id(), $tr->stable_id());
throw("Error. Exon maps to multiple locations in peptide and those".
- " locations are not continuous." .
- " Is this exon [$e_id] a member of this transcript [$tr_id]?");
+ " locations are not continuous." .
+ " Is this exon [$e_id] a member of this transcript [$tr_id]?");
}
}
elsif(scalar(@coords) == 1) {
@@ -1401,7 +1394,7 @@ sub _merge_ajoining_coords {
}
my $new_coord = Bio::EnsEMBL::Mapper::Coordinate->new(
- $coord->id(), $start, $last_end, $coord->strand(), $coord->rank());
+ $coord->id(), $start, $last_end, $coord->strand(), $coord->rank());
return $new_coord;
}
@@ -1446,29 +1439,29 @@ sub seq {
}
if ($self->slice->is_circular() ) {
- if ( $self->slice->start > $self->slice->end) {
+ if ( $self->slice->start > $self->slice->end) {
# Normally exons overlapping chromosome origin will have negative feature start, but slice will be from 1 .. length
# But in case you got an exon attached to a sub slice try this
- my $mid_point = $self->slice()->seq_region_length() - $self->slice()->start() + 1;
- my $seq1 = $self->slice()->subseq( $self->start(), $mid_point, $self->strand() );
+ my $mid_point = $self->slice()->seq_region_length() - $self->slice()->start() + 1;
+ my $seq1 = $self->slice()->subseq( $self->start(), $mid_point, $self->strand() );
- my $seq2 = $self->slice()->subseq( $mid_point + 1, $self->end(), $self->strand() );
+ my $seq2 = $self->slice()->subseq( $mid_point + 1, $self->end(), $self->strand() );
- $seq = $self->strand() > 0 ? "$seq1$seq2" : "$seq2$seq1";
- } elsif ( $self->start < 0 || $self->start > $self->end) {
+ $seq = $self->strand() > 0 ? "$seq1$seq2" : "$seq2$seq1";
+ } elsif ( $self->start < 0 || $self->start > $self->end) {
# Normally exons overlapping chromosome origin will be 0 based, and can have negative start
# But if you go via sub_Slice it gives you chromosome based coordinates, i.e it will have start greater then end
- my $start_point = $self->slice->seq_region_length + $self->slice->start;
- my $mid_point = $self->slice->seq_region_length;
- my $seq1 = $self->slice->subseq( $self->start, $mid_point, $self->strand);
- my $seq2 = $self->slice->subseq(1, $self->end, $self->strand );
- $seq = $self->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
- } else {
+ my $start_point = $self->slice->seq_region_length + $self->slice->start;
+ my $mid_point = $self->slice->seq_region_length;
+ my $seq1 = $self->slice->subseq( $self->start, $mid_point, $self->strand);
+ my $seq2 = $self->slice->subseq(1, $self->end, $self->strand );
+ $seq = $self->strand > 0 ? "$seq1$seq2" : "$seq2$seq1";
+ } else {
# End this is the case for genes not overlapping the origin
- $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
- }
+ $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
+ }
} else {
- $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
+ $seq = $self->slice()->subseq( $self->start(), $self->end(), $self->strand() );
}
$self->{'_seq_cache'} = $seq;
@@ -1666,4 +1659,3 @@ sub type {
1;
-
--
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