Commit cb876844 authored by Pontus Larsson's avatar Pontus Larsson
Browse files

Change to conform to variation schema 58

parent 0f7a8022
......@@ -178,7 +178,7 @@ if (!defined($file)) {
# Query the MySQL database directly for transcripts with consequence types STOP_*
my $stmt = qq{
SELECT
tv.transcript_id,
tv.transcript_stable_id,
vf.variation_id,
vf.variation_name,
vf.allele_string,
......@@ -196,8 +196,8 @@ if (!defined($file)) {
while (my ($transcript_stable_id,$variation_id,$variation_name,$allele_string,$consequence_string) = $sth->fetchrow_array()) {
# Temp fix for getting stable_id from pre-58 variation database
$stmt = qq{SELECT stable_id FROM transcript_stable_id WHERE transcript_id = $transcript_stable_id LIMIT 1};
$transcript_stable_id = $cdb->dbc->db_handle->selectall_arrayref($stmt)->[0][0];
#$stmt = qq{SELECT stable_id FROM transcript_stable_id WHERE transcript_id = $transcript_stable_id LIMIT 1};
#$transcript_stable_id = $cdb->dbc->db_handle->selectall_arrayref($stmt)->[0][0];
# Get the reference allele
my ($ref_allele) = $allele_string =~ m/^([^\/]+)\//;
......
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