From 26152269f07dc8090d6f67b686b196100bf2f541 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Thu, 27 Nov 2014 15:17:26 +0000
Subject: [PATCH] ENSCORESW-1116: first attempt at storing some form of scoring
in the overlap mappings
---
.../XrefParser/RefSeqCoordinateParser.pm | 48 ++++++++++++++++++-
1 file changed, 46 insertions(+), 2 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index 4cdcd2ebce..acbb03ebc1 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -204,6 +204,10 @@ sub run_script {
foreach my $transcript_of (sort { $a->start() <=> $b->start() } @$transcripts_of) {
my %transcript_result;
my %tl_transcript_result;
+ my %transcript_to_dbid;
+ my %translation_to_dbid;
+ my %query_overlap;
+ my %target_overlap;
my $id = $transcript_of->stable_id();
if ($id =~ /^XM_/) { next; }
my $exons_of = $transcript_of->get_all_Exons();
@@ -235,11 +239,16 @@ sub run_script {
my $exon_match = 0;
my $tl_exons = $transcript->get_all_translateable_Exons();
my $tl_exon_match = 0;
+ my $overall_overlap = 0;
+ my $overall_overlap_of = 0;
+ my $tl_overall_overlap = 0;
+ my $tl_overall_overlap_of = 0;
foreach my $exon (@$exons) {
my $start = $exon->seq_region_start();
my $end = $exon->seq_region_end();
my $overlap = $rr1->overlap_size('exon', $start, $end);
+ $overall_overlap += $overlap;
$exon_match += $overlap/($end - $start + 1);
$rr2->check_and_register('exon', $start, $end);
}
@@ -248,6 +257,7 @@ sub run_script {
my $tl_start = $tl_exon->seq_region_start();
my $tl_end = $tl_exon->seq_region_end();
my $tl_overlap = $rr3->overlap_size('exon', $tl_start, $tl_end);
+ $tl_overall_overlap += $tl_overlap;
$tl_exon_match += $tl_overlap/($tl_end - $tl_start + 1);
$rr4->check_and_register('exon', $tl_start, $tl_end);
}
@@ -255,11 +265,12 @@ sub run_script {
my $exon_match_of = 0;
my $tl_exon_match_of = 0;
-# Look for oeverlap between the two sets of exons
+# Look for overlap between the two sets of exons
foreach my $exon_of (@$exons_of) {
my $start_of = $exon_of->seq_region_start();
my $end_of = $exon_of->seq_region_end();
my $overlap_of = $rr2->overlap_size('exon', $start_of, $end_of);
+ $overall_overlap_of += $overlap_of;
$exon_match_of += $overlap_of/($end_of - $start_of + 1);
}
@@ -267,6 +278,7 @@ sub run_script {
my $tl_start_of = $tl_exon_of->seq_region_start();
my $tl_end_of = $tl_exon_of->seq_region_end();
my $tl_overlap_of = $rr4->overlap_size('exon', $tl_start_of, $tl_end_of);
+ $tl_overall_overlap_of += $tl_overlap_of;
$tl_exon_match_of += $tl_overlap_of/($tl_end_of - $tl_start_of + 1);
}
@@ -275,10 +287,19 @@ sub run_script {
my $tl_score = 0;
if (scalar(@$tl_exons_of) > 0) {
$tl_score = ( ($tl_exon_match_of + $tl_exon_match)) / (scalar(@$tl_exons_of) + scalar(@$tl_exons) );
+ if ($transcript->translation) {
+ my $tl_stable_id = $transcript->translation->stable_id;
+ $translation_to_dbid{$tl_stable_id} = $transcript->translation->stable_id;
+ $query_overlap{$tl_stable_id} = $tl_overall_overlap_of/$transcript_of->translation->length();
+ $target_overlap{$tl_stable_id} = $tl_overall_overlap/$transcript->translation->length();
+ }
}
if ($transcript->biotype eq $transcript_of->biotype) {
$transcript_result{$transcript->stable_id} = $score;
+ $transcript_to_dbid{$transcript->stable_id} = $transcript->dbID;
$tl_transcript_result{$transcript->stable_id} = $tl_score;
+ $query_overlap{$transcript->stable_id} = $overall_overlap_of/$transcript_of->length() * 100;
+ $target_overlap{$transcript->stable_id} = $overall_overlap/$transcript->length() * 100;
}
}
@@ -318,6 +339,17 @@ sub run_script {
species_id => $species_id,
info_type => 'DIRECT' });
$self->add_direct_xref($xref_id, $best_id, "Transcript", "");
+ my $ensembl_id = $transcript_to_dbid{$best_id};
+ my $object_xref_id = $self->add_object_xref({
+ xref_id => $xref_id,
+ ensembl_id => $ensembl_id,
+ object_type => 'Transcript'});
+## Add 'identity_xref' to store the overlap values
+ $self->add_identity_xref({
+ object_xref_id => $object_xref_id,
+ query_identity => $query_overlap{$best_id},
+ target_identity => $target_overlap{$best_id},
+ score => $best_score });
# Also store refseq protein as direct xref for ensembl translation, if translation exists
my $ta_of = $otherf_dba->get_TranscriptAdaptor();
@@ -329,6 +361,7 @@ sub run_script {
if (defined $tl && defined $tl_of) {
if ($tl_of->seq eq $tl->seq) {
($acc, $version) = split(/\./, $tl_of->stable_id());
+ my $tl_stable_id = $tl->stable_id;
my $tl_xref_id = $self->add_xref({ acc => $acc,
version => $version,
label => $acc,
@@ -336,7 +369,18 @@ sub run_script {
source_id => $peptide_source_id,
species_id => $species_id,
info_type => 'DIRECT' });
- $self->add_direct_xref($tl_xref_id, $tl->stable_id(), "Translation", "");
+ $self->add_direct_xref($tl_xref_id, $tl_stable_id, "Translation", "");
+ my $tl_ensembl_id = $translation_to_dbid{$tl_stable_id};
+ my $tl_object_xref_id = $self->add_object_xref({
+ xref_id => $tl_xref_id,
+ ensembl_id => $tl_ensembl_id,
+ object_type => 'Translation'});
+## Add 'identity_xref' to store the overlap values
+ $self->add_identity_xref({
+ object_xref_id => $tl_object_xref_id,
+ query_identity => $query_overlap{$tl_stable_id},
+ target_identity => $target_overlap{$tl_stable_id},
+ score => $best_score });
}
}
}
--
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