From 6e52ee246b536a288a851d1de1f0c95733db890c Mon Sep 17 00:00:00 2001
From: Nick Langridge <nickl@ebi.ac.uk>
Date: Wed, 19 Oct 2011 10:57:09 +0000
Subject: [PATCH] merged updates from 64
---
.../ebi_search_dump_generic.pl | 39 ++++++++++---------
1 file changed, 21 insertions(+), 18 deletions(-)
diff --git a/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl b/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
index d903181761..e6a3893ede 100755
--- a/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
+++ b/misc-scripts/ebi_search_dump/ebi_search_dump_generic.pl
@@ -394,11 +394,13 @@ WHERE
}
# SNP query
-# my $snp_sth = eval {
-# $dbh->prepare(
-#"select distinct(vf.variation_name) from $SNPDB.transcript_variation as tv, $SNPDB.variation_feature as vf where vf.variation_feature_id = tv.variation_feature_id and tv.transcript_stable_id in(?)"
-# );
-# };
+ my $snp_sth;
+ if ($SNPDB && $DB eq 'core') {
+ $snp_sth = $dbh->prepare(
+ "select distinct(vf.variation_name) from $SNPDB.transcript_variation as tv, $SNPDB.variation_feature as vf
+ where vf.variation_feature_id = tv.variation_feature_id and tv.feature_stable_id in(?)"
+ );
+ };
my $haplotypes = $dbh->selectall_hashref(
"select gene_id from gene g, assembly_exception ae where
@@ -516,12 +518,12 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
if ( $old{'gene_id'} ) {
-# if ( $SNPDB && $DB eq 'core' ) {
-# my @transcript_stable_ids =
-# keys %{ $old{transcript_stable_ids} };
-# $snp_sth->execute("@transcript_stable_ids");
-# $old{snps} = $snp_sth->fetchall_arrayref;
-# }
+ if ( $SNPDB && $DB eq 'core' ) {
+ my @transcript_stable_ids =
+ keys %{ $old{transcript_stable_ids} };
+ $snp_sth->execute("@transcript_stable_ids");
+ $old{snps} = $snp_sth->fetchall_arrayref;
+ }
if ($want_species_orthologs) {
$old{orthologs} =
@@ -642,11 +644,11 @@ g.seq_region_id=ae.seq_region_id and ae.exc_type='HAP'", [qw(gene_id)]
}
}
-# if ( $SNPDB && $DB eq 'core' ) {
-# my @transcript_stable_ids = keys %{ $old{transcript_stable_ids} };
-# $snp_sth->execute("@transcript_stable_ids");
-# $old{snps} = $snp_sth->fetchall_arrayref;
-# }
+ if ( $SNPDB && $DB eq 'core' ) {
+ my @transcript_stable_ids = keys %{ $old{transcript_stable_ids} };
+ $snp_sth->execute("@transcript_stable_ids");
+ $old{snps} = $snp_sth->fetchall_arrayref;
+ }
if ($want_species_orthologs) {
$old{orthologs} = $ortholog_lookup->{ $old{'gene_stable_id'} };
@@ -745,8 +747,9 @@ sub geneLineXML {
{
# $unique_synonyms->{$ed_key} = 1;
+ my $encoded = encode_entities($ed_key);
$synonyms .= qq{
- <field name="${matched_db_name}_synonym">$ed_key</field>};
+ <field name="${matched_db_name}_synonym">$encoded</field>};
}
}
@@ -813,7 +816,7 @@ sub geneLineXML {
map {
$synonyms .=
qq{
- <field name="gene_synonym">$_</field> }
+ <field name="gene_synonym">} . encode_entities($_) . {</field> }
} keys %$unique_synonyms;
my $additional_fields .= qq{
--
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