From ab5e317d8de88d61ef603e24a83c0da631edd8d2 Mon Sep 17 00:00:00 2001
From: Ewan Birney <birney@sanger.ac.uk>
Date: Thu, 21 Feb 2002 15:15:09 +0000
Subject: [PATCH] added peptide ---> contig coordinate mapping on Transcript.
Not tested. Mainly to make sure I shift the code off my laptop
---
modules/Bio/EnsEMBL/Exon.pm | 42 +++++++++++++
modules/Bio/EnsEMBL/StickyExon.pm | 97 +++++++++++++++++++++++++++++++
modules/Bio/EnsEMBL/Transcript.pm | 79 +++++++++++++++++++++++++
3 files changed, 218 insertions(+)
diff --git a/modules/Bio/EnsEMBL/Exon.pm b/modules/Bio/EnsEMBL/Exon.pm
index 86bc4af599..5e5c910725 100755
--- a/modules/Bio/EnsEMBL/Exon.pm
+++ b/modules/Bio/EnsEMBL/Exon.pm
@@ -1224,6 +1224,48 @@ sub get_cdna {
return $temp_seq;
}
+=head1
+
+ Arg 1 : integer start - relative to the exon
+ Arg 2 : integer end - relative to the exon
+
+ Function : Provides a list of Bio::EnsEMBL::SeqFeatures which
+ is the genomic coordinates of this start/end on the exon
+ For simple exons this is one feature - for Stickies this
+ is overridden
+
+ Returns : list of Bio::EnsEMBL::SeqFeature
+
+
+=cut
+
+sub contig_seqfeatures_from_relative_position {
+ my ($self,$start,$end) = @_;
+
+ if( !defined $end ) {
+ $self->throw("Have not defined all the methods!");
+ }
+
+ # easy
+ if( $start < 1 ) {
+ $self->warn("Attempting to fetch start less than 1 ($start)");
+ $start = 1;
+ }
+
+ if( $end > $self->length ) {
+ $self->warn("Attempting to fetch end greater than end of exon ($end)");
+ $end = $self->length;
+ }
+
+ my $sf = Bio::EnsEMBL::SeqFeature->new();
+ $sf->start($self->start + $start -1);
+ $sf->end($self->start + $end -1 );
+ $sf->strand($self->strand);
+ $sf->seqname($self->contig->id);
+
+ return ($sf);
+}
+
# Inherited methods
# but you do have all the SeqFeature documentation: reproduced here
diff --git a/modules/Bio/EnsEMBL/StickyExon.pm b/modules/Bio/EnsEMBL/StickyExon.pm
index 6f29ee15f4..2904b5cdd4 100755
--- a/modules/Bio/EnsEMBL/StickyExon.pm
+++ b/modules/Bio/EnsEMBL/StickyExon.pm
@@ -123,6 +123,103 @@ sub each_component_Exon{
}
+
+=head1
+
+ Arg 1 : integer start - relative to the exon
+ Arg 2 : integer end - relative to the exon
+
+ Function : Provides a list of Bio::EnsEMBL::SeqFeatures which
+ is the genomic coordinates of this start/end on the exon
+ For simple exons this is one feature for Stickies this
+ is overridden and gives out a list of Bio::EnsEMBL::SeqFeatures
+
+ Returns : list of Bio::EnsEMBL::SeqFeature
+
+
+=cut
+
+sub contig_seqfeatures_from_relative_position {
+ my ($self,$start,$end) = @_;
+
+ if( !defined $end ) {
+ $self->throw("Have not defined all the methods!");
+ }
+
+ # easy
+ if( $start < 1 ) {
+ $self->warn("Attempting to fetch start less than 1 ($start)");
+ $start = 1;
+ }
+
+ if( $end > $self->length ) {
+ $self->warn("Attempting to fetch end greater than end of exon ($end)");
+ $end = $self->length;
+ }
+
+ my @out;
+ my $sf;
+ my @exons = $self->each_component_Exon();
+ my $len = 0;
+ while( scalar(@exons) > 0 ) {
+ if( $exons[0]->length + $len > $start ) {
+ last;
+ } else {
+ my $discard = shift @exons;
+ $len += $discard;
+ }
+ }
+
+ # handle the first component exon
+
+ if( scalar(@exons) == 0 ) {
+ return @out;
+ }
+
+ $sf = Bio::EnsEMBL::SeqFeature->new();
+ $sf->seqname($exons[0]->contig->id);
+ $sf->strand($exons[0]->strand);
+ $sf->start($exons[0]->start + $start - $len);
+
+ if( $end < $len + $exons[0]->length ) {
+ $sf->end($exons[0]->start + $end - $len);
+ return $sf;
+ } else {
+ $sf->end($exons[0]->end);
+ push(@out,$sf);
+ }
+
+
+ while( scalar(@exons) ) {
+ if( $exons[0]->length + $len > $end ) {
+ last;
+ }
+ $sf = Bio::EnsEMBL::SeqFeature->new();
+ $sf->seqname($exons[0]->contig->id);
+ $sf->strand($exons[0]->strand);
+ $sf->start($exons[0]->start);
+ $sf->start($exons[0]->end);
+ push(@out,$sf);
+ $len += $exons[0]->length;
+ }
+
+ if( scalar(@exons) == 0 ) {
+ return @out;
+ }
+
+ # handle the last exon
+
+ $sf = Bio::EnsEMBL::SeqFeature->new();
+ $sf->seqname($exons[0]->contig->id);
+ $sf->strand($exons[0]->strand);
+ $sf->start($exons[0]->start);
+ $sf->start($exons[0]->start + $end - $len);
+
+
+
+ return @out;
+}
+
=head2 add_component_Exon
Title : add_component_Exon
diff --git a/modules/Bio/EnsEMBL/Transcript.pm b/modules/Bio/EnsEMBL/Transcript.pm
index 8a824baebb..967b23c01d 100755
--- a/modules/Bio/EnsEMBL/Transcript.pm
+++ b/modules/Bio/EnsEMBL/Transcript.pm
@@ -1192,6 +1192,85 @@ sub pep_coords {
+=head1
+
+ Arg 1 : integer start - relative to peptide
+ Arg 2 : integer end - relative to peptide
+
+ Function : Provides a list of Bio::EnsEMBL::SeqFeatures which
+ is the genomic coordinates of this start/end on the peptide
+
+
+ Returns : list of Bio::EnsEMBL::SeqFeature
+
+=cut
+
+sub convert_peptide_coordinate_to_contig {
+ my ($self,$start,$end) = @_;
+
+ if( !defined $end ) {
+ $self->throw("Must call with start/end");
+ }
+
+ # move start end into translate cDNA coordinates now.
+ # much easier!
+ $start = 3* $start;
+ $end = 3* $end;
+
+ if( !defined $self->translation ) {
+ $self->throw("No translation, so no peptide coordinate!");
+ }
+
+ # get out exons, walk along until we hit first exon
+ # calculate remaining distance.
+
+ my $start_exon;
+ my @exons = $self->get_all_Exons;
+ while( my $exon = shift @exons ) {
+ if( $exon = $self->translation->start_exon ) { # in memory reliance
+ my $start_exon = $exon;
+ last;
+ }
+ }
+
+ my $current_len_exon = $start_exon->length - $self->translation->start -1;
+ my $trans_len = 0;
+ my @out;
+
+ my $offset_into_exon = $self->translation->start;
+
+ my $exon;
+ while( $exon = shift @exons && $start < $trans_len + $current_len_exon ) {
+ ;
+ }
+
+ unshift(@exons,$exon);
+
+ # main loop!
+ while( my $exon = shift @exons && $end < $trans_len + $current_len_exon ) {
+ # definitely want something in this exon. Find start position
+ my $start_in_exon;
+ my $end_in_exon;
+
+ if( $start > $trans_len ) {
+ $start_in_exon = $offset_into_exon + $start - $trans_len +1;
+ } else {
+ $start_in_exon = $offset_into_exon;
+ }
+
+ if( $end < $trans_len + $current_len_exon ) {
+ $end_in_exon = $offset_into_exon -1 + ($end - $trans_len+1);
+ } else {
+ $end_in_exon = $exon->length;
+ }
+
+
+ # the main reason for make this an attribute of the exon is to handle stickies
+ push(@out,$exon->contig_seqfeatures_from_relative_position($start_in_exon,$end_in_exon));
+ }
+
+ return @out;
+}
sub find_coord {
my ($self,$coord,$type) = @_;
--
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