From e6f80908db5b4f1fc8312735ec213170412c3938 Mon Sep 17 00:00:00 2001
From: Graham McVicker <mcvicker@sanger.ac.uk>
Date: Wed, 5 Mar 2003 15:58:04 +0000
Subject: [PATCH] coding_start/end => coding_region_start/end
---
modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm | 8 +-
modules/Bio/EnsEMBL/PredictionTranscript.pm | 58 ++++------
modules/Bio/EnsEMBL/Transcript.pm | 117 ++++++++++++++------
modules/t/predictionTranscript.t | 13 +--
modules/t/transcript.t | 18 +--
5 files changed, 119 insertions(+), 95 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
index baac7c5d00..767574030c 100644
--- a/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
+++ b/modules/Bio/EnsEMBL/Lite/GeneAdaptor.pm
@@ -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(),
$tr->external_name() );
diff --git a/modules/Bio/EnsEMBL/PredictionTranscript.pm b/modules/Bio/EnsEMBL/PredictionTranscript.pm
index d4711899a2..3f22c41610 100644
--- a/modules/Bio/EnsEMBL/PredictionTranscript.pm
+++ b/modules/Bio/EnsEMBL/PredictionTranscript.pm
@@ -133,7 +133,7 @@ sub stable_id {
-=head2 coding_start
+=head2 coding_region_start
Arg [1] : The new coding start of this prediction transcript in slice
coords.
@@ -142,32 +142,32 @@ sub stable_id {
and so that it can be drawn as a Transcript. Since prediction
transcripts do not currently have UTRs the coding start should
return the same value as the start method.
- By convention, the coding_start is always lower than the value
- returned by the coding_end method. The value returned by this
- function is NOT the biological coding start since on the
- reverse strand the biological coding start would be the
- higher genomic value.
+ By convention, the coding_region_start is always lower than the
+ value returned by the coding_region_end method. The value
+ returned by this function is NOT the biological coding start
+ since on the reverse strand the biological coding start would
+ be the higher genomic value.
Returntype: scalar int
Exceptions: none
Caller : GlyphSet_transcript
=cut
-sub coding_start {
+sub coding_region_start {
my ($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
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index be0bfecf92..305f83314d 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -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;
diff --git a/modules/t/predictionTranscript.t b/modules/t/predictionTranscript.t
index d5413280da..621c69c10e 100644
--- a/modules/t/predictionTranscript.t
+++ b/modules/t/predictionTranscript.t
@@ -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'));
diff --git a/modules/t/transcript.t b/modules/t/transcript.t
index e4debf3f43..125e329f8f 100644
--- a/modules/t/transcript.t
+++ b/modules/t/transcript.t
@@ -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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