From 2c378673427c472d4cefbd9c34abca42ac68875f Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Thu, 2 Nov 2006 09:32:54 +0000
Subject: [PATCH] Added removal of promiscuous probesets
---
.../probe_mapping/probe2transcript.pl | 40 +++++++++----------
1 file changed, 19 insertions(+), 21 deletions(-)
diff --git a/misc-scripts/probe_mapping/probe2transcript.pl b/misc-scripts/probe_mapping/probe2transcript.pl
index 8f1a2b4269..3c9ef835f6 100644
--- a/misc-scripts/probe_mapping/probe2transcript.pl
+++ b/misc-scripts/probe_mapping/probe2transcript.pl
@@ -71,7 +71,7 @@ my %exonic_probesets;
my %utr_probesets;
my %intronic_probesets;
-my %promiscuous_probes;
+my %promiscuous_probesets;
my %dbentries_per_probeset;
my $i = 0;
@@ -102,6 +102,9 @@ foreach my $transcript (@{$transcript_adaptor->fetch_all()}) {
foreach my $feature (@$oligo_features) {
my $probeset = $feature->probeset();
+
+ next if ($promiscuous_probesets{$probeset});
+
my $probe = $feature->probe();
my $probe_length = $probe->probelength();
my $min_overlap = ($probe_length - $max_mismatches);
@@ -206,40 +209,37 @@ sub add_xref {
# $dbe->dbID:$transcript->dbID
push @{$dbentries_per_probeset{$probeset}}, $dbe->dbID() . ":" . $transcript->dbID();
+ # if any probesets map to more than 100 transcripts, ignore them in future and
+ # delete existing mappings to them
+ if (scalar(@{$dbentries_per_probeset{$probeset}}) > $max_probesets_per_transcript) {
+ $promiscuous_probesets{$probeset} = $probeset;
+ remove_probeset_transcript_mappings($t_db, $probeset);
+ }
}
}
# ----------------------------------------------------------------------
-# Remove mappings for probesets that map to more than 100 transcripts
+# Remove mappings for a particular probeset
-# TODO This is horribly inefficent, potentially thousands of unnecessary db calls
+sub remove_probeset_transcript_mappings {
-sub prune_promiscuous_probesets {
+ my ($dba, $probeset) = @_;
- my ($dba) = @_;
-
- print "Removing probesets that map to more than $max_probesets_per_transcript transcripts\n";
+ print "Removing probeset $probeset\n";
my $p = 0;
my $sth = $dba->dbc()->prepare("DELETE FROM object_xref WHERE xref_id=? AND ensembl_object_type='Transcript' AND ensembl_id=?");
- foreach my $probeset (keys %dbentries_per_probeset) {
-
- my $values = @{$dbentries_per_probeset{$probeset}};
+ my $values = @{$dbentries_per_probeset{$probeset}};
- if ($values > $max_probesets_per_transcript) {
+ foreach my $value (@{$dbentries_per_probeset{$probeset}}) {
- foreach my $value (@{$dbentries_per_probeset{$probeset}}) {
+ my ($dbe_id, $transcript_id) = split(/:/, $value);
- my ($dbe_id, $transcript_id) = split(/:/, $value);
-
- $sth->execute($dbe_id, $transcript_id);
- $p++;
- }
-
- }
+ $sth->execute($dbe_id, $transcript_id);
+ $p++;
}
@@ -247,8 +247,6 @@ sub prune_promiscuous_probesets {
print "Removed $p probeset-transcript mappings\n";
- # TODO - remove any xrefs that have 0 object_xrefs?
-
}
# ----------------------------------------------------------------------
--
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