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Commit e6f80908 authored by Graham McVicker's avatar Graham McVicker
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coding_start/end => coding_region_start/end

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......@@ -491,8 +491,8 @@ sub _objects_from_sth {
my $transcript = Bio::EnsEMBL::Transcript->new();
$transcript->adaptor( $core_db_adaptor->get_TranscriptAdaptor() );
$transcript->dbID( $hr->{'transcript_id'});
$transcript->coding_start( $coding_start );
$transcript->coding_end( $coding_end );
$transcript->coding_region_start( $coding_start );
$transcript->coding_region_end( $coding_end );
$transcript->stable_id( $hr->{ 'transcript_name' });
$transcript->type( $hr->{ 'type' } );
$transcript->external_status( $hr->{'external_status'} );
......@@ -831,8 +831,8 @@ sub store {
$sth->execute( $gene->source(), $gene->analysis()->logic_name(),
$gene->type, $tr->dbID(), $tr->stable_id, $gene->chr_name,
$tr->start(), $tr->end(), $gene->strand(), $tr->coding_start(),
$tr->coding_end(), $tr->translation->dbID(),
$tr->start(), $tr->end(), $gene->strand(), $tr->coding_region_start(),
$tr->coding_region_end(), $tr->translation->dbID(),
$tr->translation->stable_id(), $gene->dbID(), $gene->stable_id(),
$exon_structure, $exon_ids, $tr->external_db(), $tr->external_status(),
$tr->external_name() );
......
......@@ -133,7 +133,7 @@ sub stable_id {
=head2 coding_start
=head2 coding_region_start
Arg [1] : The new coding start of this prediction transcript in slice
coords.
......@@ -142,32 +142,32 @@ sub stable_id {
and so that it can be drawn as a Transcript. Since prediction
transcripts do not currently have UTRs the coding start should
return the same value as the start method.
By convention, the coding_start is always lower than the value
returned by the coding_end method. The value returned by this
function is NOT the biological coding start since on the
reverse strand the biological coding start would be the
higher genomic value.
By convention, the coding_region_start is always lower than the
value returned by the coding_region_end method. The value
returned by this function is NOT the biological coding start
since on the reverse strand the biological coding start would
be the higher genomic value.
Returntype: scalar int
Exceptions: none
Caller : GlyphSet_transcript
=cut
sub coding_start {
sub coding_region_start {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{'coding_start'} = $arg;
} elsif(!defined $self->{'coding_start'}) {
$self->{'coding_region_start'} = $arg;
} elsif(!defined $self->{'coding_region_start'}) {
#if the coding start is not defined, use the start of the transcript
return $self->start();
}
return $self->{'coding_start'};
return $self->{'coding_region_start'};
}
=head2 coding_end
=head2 coding_region_end
Arg [1] : (optional) The new coding end of this prediction transcript
in slice coords.
......@@ -176,27 +176,27 @@ sub coding_start {
and so that it can be drawn as a Transcript. Since prediction
transcripts do not currently have UTRs the coding end should
be the same as the end of the transcript.
By convention, the coding_start is always lower than the value
returned by the coding_end method. The value returned by this
function is NOT the biological coding start since on the
reverse strand the biological coding start would be the
higher genomic value.
By convention, the coding_region_start is always lower than the
value returned by the coding_region_end method. The value
returned by this function is NOT the biological coding start
since on the reverse strand the biological coding start would
be the higher genomic value.
Returntype: scalar int
Exceptions: none
Caller : GlyphSet_transcript
=cut
sub coding_end {
sub coding_region_end {
my ($self, $arg) = @_;
if(defined $arg) {
$self->{'coding_end'} = $arg;
} elsif(!defined $self->{'coding_end'}) {
$self->{'coding_region_end'} = $arg;
} elsif(!defined $self->{'coding_region_end'}) {
#if the coding end is not defined, use the end of the transcript
return $self->end();
}
return $self->{'coding_end'};
return $self->{'coding_region_end'};
}
......@@ -351,7 +351,7 @@ sub get_all_Exons {
thus all exons are entirely translateable.
Returntype : listref of Bio::EnsEMBL::Exon
Exceptions : none
Caller : Embl_Dumper
Caller : general
=cut
......@@ -783,22 +783,6 @@ sub _get_cdna_coord_mapper {
}
# debug helper
sub _dump {
my $self = shift;
my $res = "";
if( ! defined $self->{'_exon_align'} ) {
$self->get_cdna();
}
for my $ex ( @{$self->{'_exon_align'}} ) {
$res .= "pep: ".$ex->{'pep_start'}." ".$ex->{pep_end}."\n";
$res .= "exon: ".$ex->{'exon'}->start()." ".$ex->{'exon'}->end().
" ".$ex->{'exon'}->strand()."\n";
}
return $res;
}
=head2 type
......
......@@ -38,11 +38,6 @@ Manipulation:
Email questions to the ensembl developer mailing list <ensembl-dev@ebi.ac.uk>
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
......@@ -537,7 +532,7 @@ sub cdna_coding_start {
=head2 cdna_coding_end
Arg [1] : (optional) $value
Example : $cdna_coding_end = $transcript->coding_end;
Example : $cdna_coding_end = $transcript->cdna_coding_end;
Description: Retrieves the end of the coding region of this transcript in
cdna coordinates (relative to the five prime end of the
transcript, excluding introns, including utrs).
......@@ -575,29 +570,30 @@ sub cdna_coding_end {
=head2 coding_start
=head2 coding_region_start
Arg [1] : (optional) $value
Example : $coding_start = $transcript->coding_start
Example : $coding_region_start = $transcript->coding_region_start
Description: Retrieves the start of the coding region of this transcript
in genomic coordinates (i.e. in either slice or contig coords).
By convention, the coding_start is always lower than the value
returned by the coding_end method. The value returned by this
function is NOT the biological coding start since on the
reverse strand the biological coding start would be the
higher genomic value.
By convention, the coding_region_start is always lower than
the value returned by the coding_end method.
The value returned by this function is NOT the biological
coding start since on the reverse strand the biological coding
start would be the higher genomic value.
Returntype : int
Exceptions : none
Caller : general
=cut
sub coding_start {
sub coding_region_start {
my ($self, $value) = @_;
if( defined $value ) {
$self->{'coding_start'} = $value;
} elsif(!defined $self->{'coding_start'} && defined $self->translation) {
$self->{'coding_region_start'} = $value;
} elsif(!defined $self->{'coding_region_start'} &&
defined $self->translation) {
#calculate the coding start from the translation
my $start;
my $strand = $self->translation()->start_Exon->strand();
......@@ -608,40 +604,41 @@ sub coding_start {
$start = $self->translation()->end_Exon->end();
$start -= ( $self->translation()->end() - 1 );
}
$self->{'coding_start'} = $start;
$self->{'coding_region_start'} = $start;
}
return $self->{'coding_start'};
return $self->{'coding_region_start'};
}
=head2 coding_end
=head2 coding_region_end
Arg [1] : (optional) $value
Example : $coding_end = $transcript->coding_end
Example : $coding_region_end = $transcript->coding_region_end
Description: Retrieves the start of the coding region of this transcript
in genomic coordinates (i.e. in either slice or contig coords).
By convention, the coding_end is always higher than the value
returned by the coding_start method. The value returned by this
function is NOT the biological coding start since on the
reverse strand the biological coding end would be the
lower genomic value.
By convention, the coding_region_end is always higher than the
value returned by the coding_region_start method.
The value returned by this function is NOT the biological
coding start since on the reverse strand the biological coding
end would be the lower genomic value.
Returntype : int
Exceptions : none
Caller : general
=cut
sub coding_end {
sub coding_region_end {
my ($self, $value ) = @_;
my $strand;
my $end;
if( defined $value ) {
$self->{'coding_end'} = $value;
} elsif( ! defined $self->{'coding_end'} && defined $self->translation() ) {
$self->{'coding_region_end'} = $value;
} elsif( ! defined $self->{'coding_region_end'}
&& defined $self->translation() ) {
$strand = $self->translation()->start_Exon->strand();
if( $strand == 1 ) {
$end = $self->translation()->end_Exon->start();
......@@ -650,10 +647,10 @@ sub coding_end {
$end = $self->translation()->start_Exon->end();
$end -= ( $self->translation()->start() - 1 );
}
$self->{'coding_end'} = $end;
$self->{'coding_region_end'} = $end;
}
return $self->{'coding_end'};
return $self->{'coding_region_end'};
}
......@@ -956,14 +953,18 @@ sub get_all_SNPs {
if($snp->end >= $e->start && $snp->start <= $e->end) {
#this snp is in an exon
if(($trans_strand == 1 && $snp->end < $transcript->coding_start) ||
($trans_strand == -1 && $snp->start > $transcript->coding_end)) {
if(($trans_strand == 1 &&
$snp->end < $transcript->coding_region_start) ||
($trans_strand == -1 &&
$snp->start > $transcript->coding_region_end)) {
#this snp is in the 5' UTR
$key = 'five prime UTR';
}
elsif(($trans_strand == 1 && $snp->start > $transcript->coding_end)||
($trans_strand == -1 && $snp->end < $transcript->coding_start)) {
elsif(($trans_strand == 1 &&
$snp->start > $transcript->coding_region_end)||
($trans_strand == -1 &&
$snp->end < $transcript->coding_region_start)) {
#this snp is in the 3' UTR
$key = 'three prime UTR';
}
......@@ -1093,8 +1094,8 @@ sub get_all_cdna_SNPs {
sub flush_Exons{
my ($self,@args) = @_;
$self->{'_exon_coord_mapper'} = undef;
$self->{'coding_start'} = undef;
$self->{'coding_end'} = undef;
$self->{'coding_region_start'} = undef;
$self->{'coding_region_end'} = undef;
$self->{'_start'} = undef;
$self->{'_end'} = undef;
$self->{'_strand'} = undef;
......@@ -1868,4 +1869,48 @@ sub species {
}
=head2 coding_start
Arg [1] : none
Example : none
Description: DEPRECATED use coding_region_start instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub coding_start {
my ($self, @args) = @_;
$self->warn("coding_start has been renamed coding_region_start\n" .
join(':'. caller));
return $self->coding_region_start(@args);
}
=head2 coding_end
Arg [1] : none
Example : none
Description: DEPRECATED use coding_region_end instead
Returntype : none
Exceptions : none
Caller : none
=cut
sub coding_end {
my ($self, @args) = @_;
$self->warn("coding_end has been renamed coding_region_end\n" .
join(':',caller));
return $self->coding_region_end(@args);
}
1;
......@@ -5,7 +5,7 @@ use lib 't';
BEGIN { $| = 1;
use Test;
plan tests => 33;
plan tests => 32;
}
use MultiTestDB;
......@@ -59,12 +59,12 @@ ok($pt->stable_id =~ /(\w+\.\d+\.\d+\.\d+)\.(\d+)\.(\d+)/);
#
# 6 test coding start
#
ok(&TestUtils::test_getter_setter($pt, 'coding_start', 6));
ok(&TestUtils::test_getter_setter($pt, 'coding_region_start', 6));
#
# 7 test coding end
#
ok(&TestUtils::test_getter_setter($pt, 'coding_end', 7));
ok(&TestUtils::test_getter_setter($pt, 'coding_region_end', 7));
#
......@@ -205,12 +205,7 @@ ok($defined_exons_count == $pt->cdna2genomic($cstart, $cend));
#
# 32 test _dump executes
#
ok($pt->_dump || 1);
#
# 33 test type
# 32 test type
#
ok(&TestUtils::test_getter_setter($pt, 'type', 'test'));
......@@ -40,8 +40,8 @@ for my $gene ( @$genes ) {
debug( $trans->stable_id()." does not translate." );
last;
}
if( $trans->coding_start() != $trans->start() &&
$trans->coding_end() != $trans->end() ) {
if( $trans->coding_region_start() != $trans->start() &&
$trans->coding_region_end() != $trans->end() ) {
$utr_trans = $trans->stable_id();
}
}
......@@ -100,11 +100,11 @@ ok( substr( $tr->spliced_seq(), 0, 10 ) eq "ACGAGACGAA" );
debug( "translateable_seq->substr == \"".substr( $tr->translateable_seq(),0,10 )."\"" );
ok( substr( $tr->translateable_seq(),0,10 ) eq "ATGGCAGTGA" );
debug( "coding_start() == ".$tr->coding_start() );
ok( $tr->coding_start() == 85834 );
debug( "coding_region_start() == ".$tr->coding_region_start() );
ok( $tr->coding_region_start() == 85834 );
debug( "coding_end() == ".$tr->coding_end() );
ok( $tr->coding_end() == 108631 );
debug( "coding_region_end() == ".$tr->coding_region_end() );
ok( $tr->coding_region_end() == 108631 );
debug( "pep2genomic: ".($tr->pep2genomic( 10,20 ))[0]->start());
my @pepcoords = $tr->pep2genomic( 10, 20 );
......@@ -116,11 +116,11 @@ my $t_strand = $tr->get_all_Exons->[0]->strand;
my $pep_len = ($tr->cdna_coding_end - $tr->cdna_coding_start + 1) / 3;
my $coord_num = 0;
my $coding_start = $tr->coding_start;
my $coding_end = $tr->coding_end;
my $coding_region_start = $tr->coding_region_start;
my $coding_region_end = $tr->coding_region_end;
#expect coordinate for each exon with coding sequence
foreach my $e (@{$tr->get_all_Exons}) {
if($e->end > $coding_start && $e->start < $coding_end) {
if($e->end > $coding_region_start && $e->start < $coding_region_end) {
$coord_num++;
}
}
......
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