XrefMapper::ProcessPrioritys Class Reference
Public Member Functions | |
| public | new () |
| public | get_priority_names () |
| public | process () |
| public | process_dependents () |
| protected | _detach_object_xref () |
Detailed Description
Definition at line 7 of file ProcessPrioritys.pm.
Member Function Documentation
◆ _detach_object_xref()
| protected XrefMapper::ProcessPrioritys::_detach_object_xref | ( | ) |
Undocumented method
Code:
click to view
sub _detach_object_xref {
my $self = shift;
my ($xref_id, $dep_xref_id, $object_type, $ensembl_id, $dbi) = @_;
# Drop all the identity and go xrefs for the dependents of an xref
my $remove_dep_ox_sth = $dbi->prepare(
"DELETE ix FROM object_xref ox \
LEFT JOIN identity_xref ix ON ix.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 = $dbi->prepare(
"UPDATE IGNORE object_xref SET ox_status = 'FAILED_PRIORITY' \
WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ox_status = 'DUMP_OUT' AND ensembl_id = ?"
);
# This deletes everything left behind by the previous query.
my $clean_dep_ox_sth = $dbi->prepare(
"DELETE FROM object_xref \
WHERE master_xref_id = ? AND ensembl_object_type = ? AND xref_id = ? AND ox_status = 'DUMP_OUT' AND ensembl_id = ?"
);
$remove_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $ensembl_id);
# change status of object_xref to FAILED_PRIORITY for record keeping
$update_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $ensembl_id);
# delete the duplicates.
$clean_dep_ox_sth->execute($xref_id, $object_type, $dep_xref_id, $ensembl_id);
$remove_dep_ox_sth->finish();
$update_dep_ox_sth->finish();
$clean_dep_ox_sth->finish();
}
◆ get_priority_names()
| public XrefMapper::ProcessPrioritys::get_priority_names | ( | ) |
Undocumented method
Code:
click to view
sub get_priority_names{
my ($self, $dbi) = @_;
my $psth = $dbi->prepare("select s.priority_description, s.name from source s, xref x where x.source_id = s.source_id group by s.priority_description, s.name order by s.name") || die "prepare failed";
$psth->execute() || die "execute failed";
my @names;
my %seen;
my $last_name = "rubbish";
my ($desc,$name);
$psth->bind_columns(\$desc,\$name);
while($psth->fetch()){
if($name eq $last_name and !defined($seen{$name})){
push @names, $name;
$seen{$name} = 1;
}
$last_name = $name;
}
return @names;
}
◆ new()
| public XrefMapper::ProcessPrioritys::new | ( | ) |
Undocumented method
Code:
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sub new {
my($class, $mapper) = @_;
my $self ={};
bless $self,$class;
# $self->core($mapper->core);
$self->xref($mapper->xref);
$self->verbose($mapper->verbose);
return $self;
}
◆ process()
| public XrefMapper::ProcessPrioritys::process | ( | ) |
Undocumented method
Code:
click to view
sub process {
my ($self) = @_;
my $dbi = $self->xref->dbc;
my @names = $self->get_priority_names($dbi);
print "The following will be processed as priority xrefs\n" if($self->verbose);
foreach my $name (@names){
print "\t$name\n" if($self->verbose);
}
my $update_ox_sth = $dbi->prepare('update object_xref set ox_status = "FAILED_PRIORITY" where object_xref_id = ?');
my $update_x_sth = $dbi->prepare("update xref set dumped = 'NO_DUMP_ANOTHER_PRIORITY' where xref_id = ?");
# 1) Set to failed all those that have no object xrefs.
my $f_sql =(<<FSQL);
SELECT x.xref_id
FROM source s, xref x
LEFT JOIN object_xref ox ON ox.xref_id = x.xref_id
WHERE x.source_id = s.source_id
AND s.name = ?
AND ox.object_xref_id is null
FSQL
my $f_sth = $dbi->prepare($f_sql);
foreach my $name (@names){
$f_sth->execute($name);
my ($xref_id);
$f_sth->bind_columns(\$xref_id);
while($f_sth->fetch()){
$update_x_sth->execute($xref_id);
}
}
$f_sth->finish;
#
# Now ALL object_xrefs have an identity_xref :-)
# So we can do a straight join and treat all info_types the same way.
#
my $new_sql =(<<NEWS);
SELECT ox.object_xref_id, x.accession, x.xref_id, (ix.query_identity + ix.target_identity) as identity, ox.ox_status, ox.ensembl_object_type, ensembl_id, info_type
FROM object_xref ox, xref x, source s, identity_xref ix
WHERE ox.object_xref_id = ix.object_xref_id
AND ox.xref_id = x.xref_id
AND s.source_id = x.source_id
AND s.name = ?
ORDER BY x.accession DESC, s.priority ASC , identity DESC, x.xref_id DESC
NEWS
my $new_sth = $dbi->prepare($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
#
my $idx_copy_sql = (<<IDXCP);
UPDATE identity_xref SET query_identity = ?, target_identity = ?, hit_start = ?, hit_end = ?, translation_start = ?, translation_end = ?, cigar_line = ?, score = ?, evalue = ?
WHERE object_xref_id = ?;
IDXCP
my $idx_copy_sth = $dbi->prepare($idx_copy_sql);
#
# Query to copy synonyms from one xref to another
#
my $syn_copy_sql = (<<SYNCP);
INSERT IGNORE INTO synonym (SELECT ?, synonym FROM synonym
WHERE xref_id = ?);
SYNCP
my $syn_copy_sth = $dbi->prepare($syn_copy_sql);
my $best_ox_sth = $dbi->prepare("SELECT object_xref_id FROM object_xref WHERE xref_id = ? and ensembl_object_type = ? and ensembl_id = ?");
my $seq_score_sql = (<<SEQCP);
SELECT query_identity, target_identity, hit_start, hit_end, translation_start, translation_end, cigar_line, score, evalue
FROM identity_xref WHERE object_xref_id = ?
SEQCP
my $seq_score_sth = $dbi->prepare($seq_score_sql);
foreach my $name (@names){
$new_sth->execute($name);
my ($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 $seen = 0;
my @gone; # list of xref_ids that we've already seen for this accession
while($new_sth->fetch){
if($last_acc eq $acc){
if($xref_id != $best_xref_id){
$seen = ($xref_id == $last_xref_id);
$last_xref_id = $xref_id;
# If xref is a sequence_match, we want to copy the alignment identity_xref to prioritised mappings of the same ensembl_id
if ($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);
$seq_score_sth->bind_columns(\$query_identity, \$target_identity, \$hit_start, \$hit_end, \$translation_start, \$translation_end, \$cigar_line, \$score, \$evalue);
$seq_score_sth->fetch();
$best_ox_sth->execute($best_xref_id, $object_type, $ensembl_id);
$best_ox_sth->bind_columns(\$best_object_xref_id);
$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
if (!$seen) {
$update_x_sth->execute($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, $dbi);
}
}
else{ # not DUMP_OUT
$update_x_sth->execute($xref_id);
}
} else {
# Alignment did not pass, dismiss
if ($status eq 'FAILED_CUTOFF') {
next;
}
## There might be several mappings for the best priority
push @best_ensembl_id, $ensembl_id;
}
if(@gone){ #best priority failed so another one now found so set dumped;
if($last_name eq $acc){
foreach my $d (@gone){
$update_x_sth->execute($d);
}
}
}
}
else{ # NEW xref_id
if($status eq "DUMP_OUT"){
$last_acc = $acc;
$best_xref_id = $xref_id;
@best_ensembl_id = ($ensembl_id);
if(@gone and $last_name eq $acc){
foreach my $d (@gone){
$update_x_sth->execute($d);
}
@gone=();
}
}
else{ # new xref_id not DUMP_OUT
push @gone, $xref_id;
$last_name = $acc;
}
}
}
}
$new_sth->finish;
$update_ox_sth->finish;
$update_x_sth->finish;
$seq_score_sth->finish;
$best_ox_sth->finish;
$idx_copy_sth->finish;
$syn_copy_sth->finish;
my $sth = $dbi->prepare("insert into process_status (status, date) values('prioritys_flagged',now())");
$sth->execute();
$sth->finish;
}
◆ process_dependents()
| public XrefMapper::ProcessPrioritys::process_dependents | ( | ) |
Undocumented method
Code:
click to view
sub process_dependents{
# master xref IDs are entries for the current accession via various methods. We take dependent xrefs from the old and add to the new
my ($self, $old_master_xref_id, $new_master_xref_id, $dbi) = @_;
my $matching_ens_sth = $dbi->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 = $dbi->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 = $dbi->prepare("insert into dependent_xref(master_xref_id, dependent_xref_id, linkage_annotation, linkage_source_id) values(?, ?, ?, ?)");
my $insert_dep_ox_sth = $dbi->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 = $dbi->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_ix_sth = $dbi->prepare("insert ignore into identity_xref(object_xref_id, query_identity, target_identity) values(?, 100, 100)");
my @master_xrefs = ($old_master_xref_id);
my $recursive = 0;
my ($new_object_type, $new_ensembl_id, $old_object_type, $old_ensembl_id);
my ($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;
}
my %old_ensembl_ids;
$matching_ens_sth->execute($old_master_xref_id);
$matching_ens_sth->bind_columns(\$old_object_type, \$old_ensembl_id);
while ($matching_ens_sth->fetch()) {
push @{ $old_ensembl_ids{$old_object_type} }, $old_ensembl_id;
}
## Loop through all dependent xrefs of old master xref, and recurse
while(my $xref_id = pop(@master_xrefs)){
# Get dependent xrefs, be they gene, transcript or translation
$dep_sth->execute($xref_id);
$dep_sth->bind_columns(\$dep_xref_id, \$linkage_annotation, \$linkage_source_id, \$object_type);
if ($recursive) {
$new_master_xref_id = $xref_id;
}
while($dep_sth->fetch()){
# Remove all mappings to low priority xrefs
# Then delete any leftover identity or go xrefs of it
foreach my $ensembl_id (@{ $old_ensembl_ids{$object_type}} ) {
$self->_detach_object_xref($xref_id, $dep_xref_id, $object_type, $ensembl_id, $dbi);
}
# Duplicate each dependent for the new master xref if it is the first in the chain
unless ($recursive) {
$insert_dep_x_sth->execute($new_master_xref_id, $dep_xref_id, $linkage_annotation, $linkage_source_id);
}
# Loop through all chosen (best) ensembl ids mapped to priority xref, and connect them with object_xrefs
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, $object_type, $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()) {
$insert_ix_sth->execute($new_object_xref_id);
}
}
unless ($dep_xref_id == $xref_id) {
push @master_xrefs, $dep_xref_id; # remember chained dependent xrefs
}
}
$recursive = 1;
}
$matching_ens_sth->finish();
$dep_sth->finish();
$insert_dep_x_sth->finish();
$insert_dep_ox_sth->finish();
$dep_ox_sth->finish();
$insert_ix_sth->finish();
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefMapper/ProcessPrioritys.pm
