From 7c8f38a855b25c1abf6b2697d437b478926ff53c Mon Sep 17 00:00:00 2001
From: Glenn Proctor <gp1@sanger.ac.uk>
Date: Tue, 16 Jan 2007 11:49:23 +0000
Subject: [PATCH] Added check for identical oligo_array/external_db names
---
.../probe_mapping/probe2transcript.pl | 70 +++++++++++++++++--
1 file changed, 66 insertions(+), 4 deletions(-)
diff --git a/misc-scripts/probe_mapping/probe2transcript.pl b/misc-scripts/probe_mapping/probe2transcript.pl
index 8e3aa90046..f85f911df8 100644
--- a/misc-scripts/probe_mapping/probe2transcript.pl
+++ b/misc-scripts/probe_mapping/probe2transcript.pl
@@ -91,6 +91,8 @@ if ($xref_host && $xref_dbname && $xref_user) {
}
+check_names_match($oligo_db, $xref_db);
+
delete_existing_xrefs($oligo_db, $xref_db, @arrays) if ($delete);
delete_unmapped_entries($xref_db) if ($delete);
@@ -511,6 +513,64 @@ sub check_existing_and_exit {
# ----------------------------------------------------------------------
+# Check that the array names in oligo_db match the names in the external_db table in xref_db
+
+sub check_names_match {
+
+ my ($oligo_adaptor, $dbentry_adaptor) = @_;
+
+ my $mismatch;
+
+ # cache oligo_array.name entries
+ my %oligo_array_names;
+
+ my $oligo_sth = $oligo_adaptor->dbc()->prepare("SELECT DISTINCT(name) FROM oligo_array");
+ $oligo_sth->execute();
+
+ while(my @row = $oligo_sth->fetchrow_array()){
+
+ $oligo_array_names{$row[0]} = $row[0];
+
+ }
+
+ $oligo_sth->finish();
+
+ # and external_db names
+ my %external_db_names;
+ my $xref_sth = $dbentry_adaptor->dbc()->prepare("SELECT DISTINCT(db_name) FROM external_db");
+
+ $xref_sth->execute();
+ while (my @row2 = $xref_sth->fetchrow_array()) {
+
+ $external_db_names{$row2[0]} = $row2[0];
+
+ }
+
+ $xref_sth->finish();
+
+ # now compare them
+ foreach my $oligo_array_name (keys %oligo_array_names) {
+ if (!$external_db_names{$oligo_array_name}) {
+ print "$oligo_array_name appears in oligo_array but not in external_db\n";
+ $mismatch = 1;
+ }
+ }
+
+ #foreach my $external_db_name (keys %external_db_names) {
+ # if (!$oligo_array_names{$external_db_name}) {
+ # print "$external_db_name appears in external_db but not in oligo_array\n";
+ # }
+ #}
+
+ if ($mismatch) {
+ print "At least one oligo array name was found that does not appear in external_db; this needs to be rectified before this script can be run successfully.\n";
+ exit(1);
+ }
+
+}
+
+# ----------------------------------------------------------------------
+
# Remove mappings for a particular probeset
#sub remove_probeset_transcript_mappings {
@@ -565,10 +625,12 @@ sub get_or_create_analysis {
if (!$analysis) {
- $analysis = $analysis_adaptor->store(new Bio::EnsEMBL::Analysis(-logic_name => 'probe2transcript',
- -program => 'probe2transcript.pl',
- -description => 'Probe to transcript mapping',
- -displayable => '0'));
+ my $id = $analysis_adaptor->store(new Bio::EnsEMBL::Analysis(-logic_name => 'probe2transcript',
+ -program => 'probe2transcript.pl',
+ -description => 'Probe to transcript mapping',
+ -displayable => '0'));
+
+ $analysis = $analysis_adaptor->fetch_by_logic_name("probe2transcript");
}
--
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