From 3c79026df457118d3bf2c38bf007b8967f299b76 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 12 Dec 2014 09:17:49 +0000
Subject: [PATCH] Revert "ENSCORESW-1116: first attempt at storing some form of
scoring in the overlap mappings" overlap score is not identity score, we get
the identity from the alignments instead This reverts commit
26152269f07dc8090d6f67b686b196100bf2f541.
---
.../XrefParser/RefSeqCoordinateParser.pm | 48 +------------------
1 file changed, 2 insertions(+), 46 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
index fdee63dbc6..7e44052000 100644
--- a/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+++ b/misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
@@ -213,10 +213,6 @@ 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();
@@ -248,16 +244,11 @@ 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);
}
@@ -266,7 +257,6 @@ 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);
}
@@ -274,12 +264,11 @@ sub run_script {
my $exon_match_of = 0;
my $tl_exon_match_of = 0;
-# Look for overlap between the two sets of exons
+# Look for oeverlap 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);
}
@@ -287,7 +276,6 @@ 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);
}
@@ -296,19 +284,10 @@ 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;
}
}
@@ -350,17 +329,6 @@ 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();
@@ -372,7 +340,6 @@ 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,
@@ -380,18 +347,7 @@ 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", "");
- 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 });
+ $self->add_direct_xref($tl_xref_id, $tl->stable_id(), "Translation", "");
}
}
}
--
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