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Commit 37537599 authored by Kieron Taylor's avatar Kieron Taylor :angry: Committed by Magali Ruffier
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Super-tidying commit. Eliminate unnamed statement handle, don't pass fruitless... 

Super-tidying commit. Eliminate unnamed statement handle, don't pass fruitless object types, add some comments, change some others, collapse some code into neater forms
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misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
+ 30
− 35
View file @ 37537599
......@@ -129,7 +129,7 @@ FSQL
AND s.name = ?
ORDER BY x.accession DESC, s.priority ASC , identity DESC, x.xref_id DESC
NEWS
my $new_sth = $self->xref->dbc->prepare($new_sql);
#
# Query to copy identity_xref values from one xref to another
# This is to keep alignment information event if alignment was not the best match
......@@ -161,28 +161,27 @@ SYNCP
SEQCP
my $seq_score_sth = $self->xref->dbc->prepare($seq_score_sql);
my $sth = $self->xref->dbc->prepare($new_sql);
foreach my $name (@names){
$sth->execute($name);
$new_sth->execute($name);
my ($object_xref_id, $acc, $xref_id, $identity, $status, $object_type, $ensembl_id, $info_type);
$sth->bind_columns(\$object_xref_id, \$acc, \$xref_id, \$identity, \$status, \$object_type, \$ensembl_id, \$info_type);
$new_sth->bind_columns(\$object_xref_id, \$acc, \$xref_id, \$identity, \$status, \$object_type, \$ensembl_id, \$info_type);
my $last_acc = "";
my $last_name = "";
my $best_xref_id = undef;
my @best_ensembl_id = undef;
my $last_xref_id = 0;
my $seen = 0;
my @gone;
while($sth->fetch){
my @gone; # list of xref_ids that we've already seen for this accession
while($new_sth->fetch){
if($last_acc eq $acc){
if($xref_id != $best_xref_id){
if ($xref_id == $last_xref_id) {
$seen = 1;
} else {
$seen = 0;
}
# We've already seen this accession before, and this xref_id is not the best one
$seen = ($xref_id == $last_xref_id);
$last_xref_id = $xref_id;
# If it is a sequence_match, we want to copy the alignment identity_xref to prioritised mappings to the same ensembl_id
# If xref is a sequence_match, we want to copy the alignment identity_xref to prioritised mappings of the same ensembl_id
if ($info_type eq 'SEQUENCE_MATCH') {
my ($query_identity, $target_identity, $hit_start, $hit_end, $translation_start, $translation_end, $cigar_line, $score, $evalue, $best_object_xref_id);
$seq_score_sth->execute($object_xref_id);
......@@ -193,6 +192,7 @@ SEQCP
$best_ox_sth->fetch();
$idx_copy_sth->execute($query_identity, $target_identity, $hit_start, $hit_end, $translation_start, $translation_end, $cigar_line, $score, $evalue, $best_object_xref_id);
}
# If the xref is marked DUMP_OUT, set it to FAILED_PRIORITY
if($status eq "DUMP_OUT"){
$update_ox_sth->execute($object_xref_id);
## If it is the first time processing this xref_id, also process dependents and update status
......@@ -200,13 +200,13 @@ 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, $object_type, \@best_ensembl_id);
$self->process_dependents($xref_id, $best_xref_id, \@best_ensembl_id);
}
}
else{
$update_x_sth->execute($xref_id);
}
} else {
else{ # not DUMP_OUT
$update_x_sth->execute($xref_id);
}
} else {
## There might be several mappings for the best priority
push @best_ensembl_id, $ensembl_id;
}
......@@ -218,11 +218,11 @@ SEQCP
}
}
}
else{ # NEW
else{ # NEW xref_id
if($status eq "DUMP_OUT"){
$last_acc = $acc;
$best_xref_id = $xref_id;
@best_ensembl_id = ($ensembl_id);
@best_ensembl_id = ($ensembl_id);
if(@gone and $last_name eq $acc){
foreach my $d (@gone){
$update_x_sth->execute($d);
......@@ -230,19 +230,15 @@ SEQCP
@gone=();
}
}
else{
if($last_name eq $acc){
push @gone, $xref_id; }
else{
@gone = ();
push @gone, $xref_id;
}
$last_name = $acc;
}
else{ # new xref_id not DUMP_OUT
if ($last_name ne $acc) { @gone = () } # new accession
push @gone, $xref_id;
$last_name = $acc;
}
}
}
}
$sth->finish;
$new_sth->finish;
$update_ox_sth->finish;
$update_x_sth->finish;
......@@ -251,18 +247,16 @@ SEQCP
$idx_copy_sth->finish;
$syn_copy_sth->finish;
$sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('prioritys_flagged',now())");
my $sth = $self->xref->dbc->prepare("insert into process_status (status, date) values('prioritys_flagged',now())");
$sth->execute();
$sth->finish;
}
sub process_dependents{
my ($self, $old_master_xref_id, $new_master_xref_id, $object_type, $best_ensembl_ids) = @_;
my ($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
# $object_type may not correspond to all of the $best_ensembl_ids, only some. This is where the GO xref problem arises for Zebrafish
# Get $object_type from object_xref of new_master_xref instead of trusting calling code
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 $insert_dep_x_sth = $self->xref->dbc->prepare("insert into dependent_xref(master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) values(?, ?, ?, ?)");
......@@ -311,8 +305,8 @@ sub process_dependents{
# 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
# 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};
# Add new object_xref for each best_ensembl_id.
......@@ -358,7 +352,6 @@ sub _get_old_ensembl_ids_associated_with_xref {
$old_ens_id_sth->execute($old_master_xref_id);
$old_ens_id_sth->bind_columns(\$old_ensembl_id);
my $skip = 0;
while ($old_ens_id_sth->fetch()) {
unless (exists $new_id_lookup{$old_ensembl_id}) {
push @old_ensembl_ids, $old_ensembl_id;
......@@ -374,12 +367,14 @@ sub _detach_object_xref {
my $self = shift;
my ($xref_id, $dep_xref_id, $ids, $splonk) = @_;
my %id_type_hash = %$splonk;
# 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 = ?"
);
# 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' \
......
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