From 38f511961b64e4ee1bc215e3b034bbb7ae542473 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 9 Jan 2012 15:15:34 +0000
Subject: [PATCH] Don't remove core data if status is moved back to
mapping_finished. Changes to alt_alleles: use the first non-reference gene if
there is no reference gene in an alt_allele.
---
.../xref_mapping/XrefMapper/BasicMapper.pm | 102 ++++++++----------
1 file changed, 46 insertions(+), 56 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
index 51427d8ede..f1f37b69a1 100644
--- a/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
@@ -533,13 +533,16 @@ sub get_alt_alleles {
my $gene_id;
my $alt_id;
- my $sth = $self->core->dbc->prepare("select alt_allele_id, gene_id from alt_allele");
+ my $is_ref;
+ my $sth = $self->core->dbc->prepare("select alt_allele_id, gene_id, is_ref from alt_allele");
$sth->execute;
- $sth->bind_columns(\$alt_id,\$gene_id);
+ $sth->bind_columns(\$alt_id,\$gene_id, \$is_ref);
my $count = 0 ;
my %alt_id_to_gene_id;
my %gene_id_to_alt_id;
my $max_alt_id = 0;
+ my %is_reference;
+
while($sth->fetch){
$count++;
push @{$alt_id_to_gene_id{$alt_id}}, $gene_id;
@@ -547,52 +550,36 @@ sub get_alt_alleles {
if($alt_id > $max_alt_id){
$max_alt_id = $alt_id;
}
+ if ($is_ref) {
+ $is_reference{$gene_id} = 1;
+ }
}
my $insert_sth = $self->xref->dbc->prepare("insert into alt_allele (alt_allele_id, gene_id, is_reference) values (?, ?,?)");
-
-
if($count){
- my %non_reference;
-
- my $sql = (<<"SEQ");
-SELECT g.gene_id
- FROM gene g, seq_region_attrib sra, attrib_type at
- WHERE g.seq_region_id = sra.seq_region_id AND
- at.attrib_type_id = sra.attrib_type_id AND
- at.code = 'non_ref'
-SEQ
-
- $sth = $self->core->dbc->prepare($sql);
- $sth->execute;
- $sth->bind_columns(\$gene_id);
- while($sth->fetch()){
- $non_reference{$gene_id} = 1;
- }
-
+
$sth = $self->xref->dbc->prepare("delete from alt_allele");
$sth->execute;
-
my $alt_added = 0;
my $num_of_genes = 0;
my $alt_failed = 0;
foreach my $alt_id (keys %alt_id_to_gene_id){
- # make sure one and only one is on the reference
+ # make sure only one gene or none are on the reference
my $ref_count = 0;
foreach my $gene (@{$alt_id_to_gene_id{$alt_id}}){
- if(!defined($non_reference{$gene})){
+ if(defined($is_reference{$gene})){
$ref_count++;
}
}
- if($ref_count == 1){
+ if($ref_count == 1 || $ref_count == 0){
$alt_added++;
foreach my $gene (@{$alt_id_to_gene_id{$alt_id}}){
$num_of_genes++;
my $ref =0 ;
- if(!defined($non_reference{$gene})){
+ if(defined($is_reference{$gene})){
$ref = 1;
}
$insert_sth->execute($alt_id, $gene, $ref);
@@ -894,7 +881,7 @@ sub get_species_id_from_species_name{
sub clean_up{
my $self = shift;
my $stats = shift;
-
+ my $keep_core_data = shift;
# remove all object_xref, identity_xref entries
@@ -926,27 +913,27 @@ sub clean_up{
$sth->execute();
-
- # remove all from core_info tables
- # gene_transcript_translation
- # [gene/transcript/translation]_stable_id
- #
- $sql = "DELETE from gene_transcript_translation";
- $sth = $self->xref->dbc->prepare($sql);
- $sth->execute();
+ if (!$keep_core_data) {
+ # remove all from core_info tables
+ # gene_transcript_translation
+ # [gene/transcript/translation]_stable_id
+ #
+ $sql = "DELETE from gene_transcript_translation";
+ $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute();
- $sql = "DELETE from gene_stable_id";
- $sth = $self->xref->dbc->prepare($sql);
- $sth->execute();
+ $sql = "DELETE from gene_stable_id";
+ $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute();
- $sql = "DELETE from transcript_stable_id";
- $sth = $self->xref->dbc->prepare($sql);
- $sth->execute();
-
- $sql = "DELETE from translation_stable_id";
- $sth = $self->xref->dbc->prepare($sql);
- $sth->execute();
+ $sql = "DELETE from transcript_stable_id";
+ $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute();
+ $sql = "DELETE from translation_stable_id";
+ $sth = $self->xref->dbc->prepare($sql);
+ $sth->execute();
+ }
return;
}
@@ -984,7 +971,8 @@ sub revert_to_parsing_finished{
sub revert_to_mapping_finished{
my $self = shift;
- $self->clean_up();
+
+ $self->clean_up(undef,1);
# set mapping jobs to SUBMITTED
my $sql = 'UPDATE mapping_jobs set status = "SUBMITTED"';;
@@ -1006,21 +994,23 @@ sub get_alt_allele_hashes{
my %alt_to_ref;
my %ref_to_alts;
- my $sql = "select gene_id, is_reference from alt_allele order by alt_allele_id, is_reference DESC";
+ my $sql = "select alt_allele_id, gene_id, is_reference from alt_allele order by alt_allele_id, is_reference DESC";
my $sth = $self->xref->dbc->prepare($sql);
$sth->execute();
- my ($gene_id, $is_ref);
- $sth->bind_columns(\$gene_id, \$is_ref);
+ my ($alt_allele_id,$gene_id, $is_ref);
+ $sth->bind_columns(\$alt_allele_id, \$gene_id, \$is_ref);
+ my $last_alt_allele = 0;
my $ref_gene;
while($sth->fetch()){
- if($is_ref){
- $ref_gene = $gene_id;
- }
- else{
- $alt_to_ref{$gene_id} = $ref_gene;
- push @{$ref_to_alts{$ref_gene}}, $gene_id;
- }
+ if( $alt_allele_id != $last_alt_allele) {
+ #use the first non-reference gene if there is no reference gene in an alt_allele
+ $ref_gene = $gene_id;
+ } else{
+ $alt_to_ref{$gene_id} = $ref_gene;
+ push @{$ref_to_alts{$ref_gene}}, $gene_id;
+ }
+ $last_alt_allele = $alt_allele_id;
}
$sth->finish;
--
GitLab