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Commit 3c79026d authored by Magali Ruffier's avatar Magali Ruffier
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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 26152269.
parent c8db3919
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misc-scripts/xref_mapping/XrefParser/RefSeqCoordinateParser.pm
+ 2
− 46
View file @ 3c79026d
......@@ -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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