From b2cb619b53679786cb3acfe16a8a99da39788eb0 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Mon, 8 Feb 2016 17:29:20 +0000
Subject: [PATCH] remove and add all ensembl id mappings in one go
---
.../XrefMapper/ProcessPrioritys.pm | 108 ++++++------------
1 file changed, 36 insertions(+), 72 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
index 91e9b64082..dac09b1667 100644
--- a/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
@@ -200,7 +200,7 @@ SEQCP
$update_x_sth->execute($xref_id);
# Copy synonyms across if they are missing
$syn_copy_sth->execute($best_xref_id, $xref_id);
- $self->process_dependents($xref_id, $best_xref_id, \@best_ensembl_id);
+ $self->process_dependents($xref_id, $best_xref_id);
}
}
else{ # not DUMP_OUT
@@ -253,71 +253,62 @@ SEQCP
}
sub process_dependents{
- my ($self, $old_master_xref_id, $new_master_xref_id, $best_ensembl_ids) = @_;
-
-# $best_ensembl_ids = list of e! IDs from highest priority xref for this accession
# master xref IDs are entries for the current accession via various methods. We take dependent xrefs from the old and add to the new
+ my ($self, $old_master_xref_id, $new_master_xref_id) = @_;
+
- my $dep_sth = $self->xref->dbc->prepare("select distinct dependent_xref_id, dx.linkage_annotation, dx.linkage_source_id from dependent_xref dx where dx.master_xref_id = ?");
+ my $matching_ens_sth = $self->xref->dbc->prepare("select distinct ensembl_object_type, ensembl_id from object_xref where ox_status not in ('FAILED_CUTOFF') and xref_id = ? order by ensembl_object_type");
+ my $dep_sth = $self->xref->dbc->prepare("select distinct dx.dependent_xref_id, dx.linkage_annotation, dx.linkage_source_id, ox.ensembl_object_type from dependent_xref dx, object_xref ox where ox.xref_id = dx.dependent_xref_id and ox.master_xref_id = dx.master_xref_id and dx.master_xref_id = ? order by ox.ensembl_object_type");
my $insert_dep_x_sth = $self->xref->dbc->prepare("insert into dependent_xref(master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) values(?, ?, ?, ?)");
my $insert_dep_ox_sth = $self->xref->dbc->prepare("insert ignore into object_xref(master_xref_id, ensembl_object_type, ensembl_id, linkage_type, ox_status, xref_id) values(?, ?, ?, 'DEPENDENT', 'DUMP_OUT', ?)");
my $dep_ox_sth = $self->xref->dbc->prepare("select object_xref_id from object_xref where master_xref_id = ? and ensembl_object_type = ? and ensembl_id = ? and linkage_type = 'DEPENDENT' AND ox_status = 'DUMP_OUT' and xref_id = ?");
my $insert_dep_go_sth = $self->xref->dbc->prepare("insert ignore into go_xref values(?, ?, ?)");
my $insert_ix_sth = $self->xref->dbc->prepare("insert ignore into identity_xref(object_xref_id, query_identity, target_identity) values(?, 100, 100)");
- my $get_type_sth = $self->xref->dbc->prepare("SELECT ensembl_object_type FROM object_xref WHERE ensembl_id = ? AND xref_id = ?");
my @master_xrefs = ($old_master_xref_id);
my $recursive = 0;
- my @old_ensembl_ids = $self->_get_old_ensembl_ids_associated_with_xref($old_master_xref_id, $best_ensembl_ids);
-
- # determine object type of the ensembl_ids we are taking links from and connecting to.
- my %splonk;
- foreach my $ens_id (@$best_ensembl_ids) {
- $get_type_sth->execute($ens_id,$new_master_xref_id);
- my ($type) = $get_type_sth->fetchrow_array();
- $splonk{$ens_id} = $type;
- }
- foreach my $ens_id (@old_ensembl_ids) {
- $get_type_sth->execute($ens_id,$old_master_xref_id);
- my ($type) = $get_type_sth->fetchrow_array();
- $splonk{$ens_id} = $type;
- }
+ my ($new_object_type, $new_ensembl_id);
+ my ($dep_xref_id, $linkage_annotation, $new_object_xref_id, $linkage_source_id, $object_type);
+ # Create a hash of all possible mappings for this accession
+ my %ensembl_ids;
+ $matching_ens_sth->execute($new_master_xref_id);
+ $matching_ens_sth->bind_columns(\$new_object_type, \$new_ensembl_id);
+ while ($matching_ens_sth->fetch()) {
+ push @{ $ensembl_ids{$new_object_type} }, $new_ensembl_id;
+ }
+
## Loop through all dependent xrefs of old master xref, and recurse
while(my $xref_id = pop(@master_xrefs)){
- my ($dep_xref_id, $linkage_annotation, $new_object_xref_id, $linkage_source_id);
# Get dependent xrefs, be they gene, transcript or translation
$dep_sth->execute($xref_id);
- $dep_sth->bind_columns(\$dep_xref_id, \$linkage_annotation, \$linkage_source_id);
+ $dep_sth->bind_columns(\$dep_xref_id, \$linkage_annotation, \$linkage_source_id, \$object_type);
while($dep_sth->fetch()){
- # Duplicate each dependent for the new master xref if it is the first in the chain, and detach from the original
+
+ # Remove all mappings to low priority xrefs
+ # Then delete any leftover identity or go xrefs of it
+ $self->_detach_object_xref($xref_id, $dep_xref_id, $object_type);
+
+ # Duplicate each dependent for the new master xref if it is the first in the chain
unless ($recursive) {
$insert_dep_x_sth->execute($new_master_xref_id, $dep_xref_id, $linkage_annotation, $linkage_source_id);
- # then remove any reference to master xref from the dependent xref where the new ensembl IDs are involved
- # The object type here should be decided by the dependent xref.
- $self->_detach_object_xref($xref_id, $dep_xref_id, $best_ensembl_ids,\%splonk);
}
- # also set type of object_xref from old_master_xref to FAILED_PRIORITY
- # Then delete any leftover identity or go xrefs of it
- $self->_detach_object_xref($xref_id, $dep_xref_id, \@old_ensembl_ids,\%splonk);
-
# Loop through all chosen (best) ensembl ids mapped to priority xref, and connect them with object_xrefs
- foreach my $best_ensembl_id (@$best_ensembl_ids) {
- my $e_type = $splonk{$best_ensembl_id};
+ foreach my $ensembl_id (@{ $ensembl_ids{$object_type} }) {
# Add new object_xref for each best_ensembl_id.
- $insert_dep_ox_sth->execute($new_master_xref_id, $e_type, $best_ensembl_id, $dep_xref_id);
+ $insert_dep_ox_sth->execute($new_master_xref_id, $object_type, $ensembl_id, $dep_xref_id);
## If there is a linkage_annotation, it is a go xref
if ($linkage_annotation) {
## Fetch the newly created object_xref to add them to go_xref
- $dep_ox_sth->execute($new_master_xref_id, $e_type, $best_ensembl_id, $dep_xref_id);
+ $dep_ox_sth->execute($new_master_xref_id, $object_type, $ensembl_id, $dep_xref_id);
$dep_ox_sth->bind_columns(\$new_object_xref_id);
while ($dep_ox_sth->fetch()) {
- $insert_dep_go_sth->execute($new_object_xref_id, $linkage_annotation, $new_master_xref_id);
+ $insert_dep_go_sth->execute($new_object_xref_id, $linkage_annotation, $new_master_xref_id);
$insert_ix_sth->execute($new_object_xref_id);
}
}
@@ -328,71 +319,44 @@ sub process_dependents{
$new_master_xref_id = $dep_xref_id;
}
+ $matching_ens_sth->finish();
$dep_sth->finish();
$insert_dep_x_sth->finish();
$insert_dep_ox_sth->finish();
$dep_ox_sth->finish();
$insert_dep_go_sth->finish();
$insert_ix_sth->finish();
- $get_type_sth->finish();
-}
-
-# broken out of process_dependents.
-# Get a list of IDs that are not associated with the new xref
-sub _get_old_ensembl_ids_associated_with_xref {
- my $self = shift;
- my $old_master_xref_id = shift;
- my $new_ensembl_ids = shift;
- my %new_id_lookup;
- map { $new_id_lookup{$_} = 1 } @$new_ensembl_ids;
-
- my $old_ensembl_id;
- my @old_ensembl_ids;
- my $old_ens_id_sth = $self->xref->dbc->prepare("select distinct ensembl_id from object_xref where xref_id = ?");
-
- $old_ens_id_sth->execute($old_master_xref_id);
- $old_ens_id_sth->bind_columns(\$old_ensembl_id);
- while ($old_ens_id_sth->fetch()) {
- unless (exists $new_id_lookup{$old_ensembl_id}) {
- push @old_ensembl_ids, $old_ensembl_id;
- }
- }
- $old_ens_id_sth->finish();
- return @old_ensembl_ids;
}
# Delete identity xrefs, go_xrefs for a given object xref
# Set unimportant object_xrefs to FAILED_PRIORITY, and delete all those that remain
sub _detach_object_xref {
my $self = shift;
- my ($xref_id, $dep_xref_id, $ids, $splonk) = @_;
- my %id_type_hash = %$splonk;
+ my ($xref_id, $dep_xref_id, $object_type) = @_;
# Drop all the identity and go xrefs for the dependents of an xref
my $remove_dep_ox_sth = $self->xref->dbc->prepare(
"DELETE ix, g FROM object_xref ox \
LEFT JOIN identity_xref ix ON ix.object_xref_id = ox.object_xref_id \
LEFT JOIN go_xref g ON g.object_xref_id = ox.object_xref_id \
- WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ?"
+ WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ?"
);
# Fail the object_xrefs that did link to the deleted identity/go xrefs.
# This only updates one of potentially many, due to table contraints.
my $update_dep_ox_sth = $self->xref->dbc->prepare(
"UPDATE IGNORE object_xref SET ox_status = 'FAILED_PRIORITY' \
- WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ? AND ox_status = 'DUMP_OUT'"
+ WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ox_status = 'DUMP_OUT'"
);
# This deletes everything left behind by the previous query.
my $clean_dep_ox_sth = $self->xref->dbc->prepare(
"DELETE FROM object_xref \
- WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ensembl_id = ? AND ox_status = 'DUMP_OUT'"
+ WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ox_status = 'DUMP_OUT'"
);
- foreach my $id (@$ids) {
- $remove_dep_ox_sth->execute($xref_id, $id_type_hash{$id}, $dep_xref_id, $id);
- # change status of object_xref to FAILED_PRIORITY for record keeping
- $update_dep_ox_sth->execute($xref_id, $id_type_hash{$id}, $dep_xref_id, $id);
- # delete the duplicates.
- $clean_dep_ox_sth->execute($xref_id, $id_type_hash{$id}, $dep_xref_id, $id);
- }
+ $remove_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id);
+ # change status of object_xref to FAILED_PRIORITY for record keeping
+ $update_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id);
+ # delete the duplicates.
+ $clean_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id);
$remove_dep_ox_sth->finish();
$update_dep_ox_sth->finish();
--
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