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Commit efc1c8f0 authored by Ian Longden's avatar Ian Longden
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alt allele processing added

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misc-scripts/xref_mapping/XrefMapper/BasicMapper.pm
+ 242
− 10
View file @ efc1c8f0
......@@ -1470,6 +1470,10 @@ sub biomart_testing{
}
$sth->finish;
}
my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('biomart_test_finished',now())");
$sth_stat->execute();
$sth_stat->finish;
}
......@@ -1691,35 +1695,263 @@ sub revert_to_mapping_finished{
#
sub move_xrefs_from_alt_allele_to_reference {
sub get_alt_allele_hashes{
my $self= shift;
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 $sth = $self->xref->dbc->prepare($sql);
$sth->execute();
my ($gene_id, $is_ref);
$sth->bind_columns(\$gene_id, \$is_ref);
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;
}
}
$sth->finish;
return \%alt_to_ref, \%ref_to_alts;
}
#sub move_xrefs_from_alt_allele_to_reference {
sub process_alt_alleles{
my $self = shift;
# ALL are on the Gene level now. This may change but for now it is okay.
my ($alt_to_ref, $ref_to_alts) = $self->get_alt_allele_hashes();
my $tester = XrefMapper::TestMappings->new($self);
if($tester->unlinked_entries){
die "Problems found before process_alt_alleles\n";
}
#
# Move the xrefs on to the reference Gene.
# NOTE: Igonore used as the xref might already be on this Gene already and we do not want it to crash
#
# Start with Translation
my $move_sql =(<<MOVE);
UPDATE IGNORE object_xref ox, xref x, source s
SET ox.ensembl_id = ?
WHERE x.source_id = s.source_id AND
ox.xref_id = x.xref_id AND
ox.ensembl_id = ? AND
ox.ensembl_object_type = 'Gene' AND
ox.ox_status = 'DUMP_OUT' AND
s.name in (
MOVE
$move_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
print "MOVE SQL\n$move_sql\n";
#
# Now where it was already on the Gene the ignore will have stopped the move
# so we now want to just remove those ones as they already exist.
#
my $del_ix_sql =(<<DIX);
DELETE ix
FROM identity_xref ix, object_xref ox, xref x, source s
WHERE x.source_id = s.source_id AND
ox.object_xref_id = ix.object_xref_id AND
ox.xref_id = x.xref_id AND
ox.ensembl_id = ? AND
ox.ensembl_object_type = 'Gene' AND
ox.ox_status = 'DUMP_OUT' AND
s.name in (
DIX
$del_ix_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
my $del_sql =(<<DEL);
DELETE ox
FROM object_xref ox, xref x, source s
WHERE x.source_id = s.source_id AND
ox.xref_id = x.xref_id AND
ox.ensembl_id = ? AND
ox.ensembl_object_type = 'Gene' AND
ox.ox_status = 'DUMP_OUT' AND
s.name in (
DEL
$del_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
my $move_sth = $self->xref->dbc->prepare($move_sql) || die "$move_sql cannot be prepared";
my $del_ix_sth = $self->xref->dbc->prepare($del_ix_sql) || die "$del_ix_sql cannot be prepared";
my $del_sth = $self->xref->dbc->prepare($del_sql) || die "$del_sql cannot be prepared";
my $move_count = 0;
my $del_ix_count = 0;
my $del_ox_count = 0;
foreach my $key (keys %$alt_to_ref){
$move_sth->execute($alt_to_ref->{$key}, $key);
$move_count += $move_sth->rows;
$del_ix_sth->execute($key);
$del_ix_count += $del_ix_sth->rows;
$del_sth->execute($key);
$del_ox_count += $del_sth->rows;
}
$move_sth->finish;
$del_sth->finish;
$del_ix_sth->finish;
print "Number of rows:- moved = $move_count, identitys deleted = $del_ix_count, object_xrefs deleted = $del_ox_count\n";
if($tester->unlinked_entries){
die "Problems found mid process_alt_alleles\n";
}
#
# Now we have all the data on the reference Gene we want to copy all the data
# onto the alt alleles.
#
my $get_data_sql=(<<GET);
SELECT ox.object_xref_id, ox.ensembl_object_type, ox.xref_id, ox.linkage_annotation,
ox.linkage_type, ox.ox_status, ox.unused_priority, ox.master_xref_id,
ix.query_identity, ix.target_identity, ix.hit_start, ix.hit_end,
ix.translation_start, ix.translation_end, ix.cigar_line, ix.score, ix.evalue
FROM xref x, source s, object_xref ox
LEFT JOIN identity_xref ix ON ox.object_xref_id =ix.object_xref_id
WHERE x.source_id = s.source_id AND
ox.xref_id = x.xref_id AND
ox.ensembl_id = ? AND
ox.ox_status = 'DUMP_OUT' AND
ox.ensembl_object_type = 'Gene' AND
s.name in (
GET
$get_data_sql .= "'".join("', '",$self->get_gene_specific_list()) . "')";
# select aa.is_reference, count(1) from gene_direct_xref gdx, gene_stable_id gsi, alt_allele aa where gdx.ensembl_stable_id = gsi.stable_id and gsi.internal_id = aa.gene_id group by aa.is_reference;
my $get_data_sth = $self->xref->dbc->prepare($get_data_sql) || die "Could not prepare $get_data_sql";
# select aa.is_reference, count(1) from transcript_direct_xref tdx, transcript_stable_id tsi, alt_allele aa, gene_transcript_translation gtt where tdx.ensembl_stable_id = tsi.stable_id and tsi.internal_id = gtt.transcript_id and gtt.gene_id = aa.gene_id group by aa.is_reference;
my $insert_object_xref_sql =(<<INO);
INSERT INTO object_xref (object_xref_id, ensembl_id, ensembl_object_type, xref_id, linkage_annotation,
linkage_type, ox_status, unused_priority, master_xref_id)
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?)
INO
my $insert_ox_sth = $self->xref->dbc->prepare($insert_object_xref_sql) || die "Could not prepare $insert_object_xref_sql";
#select aa.alt_allele_id, aa.is_reference, gsi.stable_id, gsi.internal_id, x.label, s.name from gene_stable_id gsi, xref x, source s, translation_direct_xref tdx, translation_stable_id tsi, alt_allele aa, gene_transcript_translation gtt where tdx.general_xref_id = x.xref_id and x.source_id = s.source_id and tdx.ensembl_stable_id = tsi.stable_id and tsi.internal_id = gtt.translation_id and gtt.gene_id = aa.gene_id and gsi.internal_id = gtt.gene_id order by aa.alt_allele_id, s.name, not aa.is_reference limit 20;
my $insert_identity_xref_sql = (<<INI);
INSERT INTO identity_xref (object_xref_id, query_identity, target_identity, hit_start, hit_end,
translation_start, translation_end, cigar_line, score, evalue )
VALUES (?, ?, ?, ?, ?, ?, ?, ?, ?, ?)
INI
my $insert_ix_sth = $self->xref->dbc->prepare($insert_identity_xref_sql) || die "Could not prepare $insert_identity_xref_sql";
my $max_object_xref_id;
my $sth = $self->xref->dbc->prepare("SELECT MAX(object_xref_id) FROM object_xref");
$sth->execute();
$sth->bind_columns(\$max_object_xref_id);
$sth->fetch;
if(!defined($max_object_xref_id) or !$max_object_xref_id){
die "Problem getting max object_xref_id";
}
$max_object_xref_id++;
my $added_count = 0;
my $ignored = 0;
foreach my $key (keys %$ref_to_alts){
$get_data_sth->execute($key);
my ($object_xref_id, $ensembl_object_type, $xref_id, $linkage_annotation,
$linkage_type, $ox_status, $unused_priority, $master_xref_id,
$query_identity, $target_identity, $hit_start, $hit_end,
$translation_start, $translation_end, $cigar_line, $score, $evalue);
$get_data_sth->bind_columns(\$object_xref_id, \$ensembl_object_type, \$xref_id, \$linkage_annotation,
\$linkage_type, \$ox_status, \$unused_priority, \$master_xref_id,
\$query_identity, \$target_identity, \$hit_start, \$hit_end,
\$translation_start, \$translation_end, \$cigar_line, \$score, \$evalue);
while( $get_data_sth->fetch()){
foreach my $alt (@{$ref_to_alts->{$key}}){
$max_object_xref_id++;
$insert_ox_sth->execute($max_object_xref_id, $alt, $ensembl_object_type, $xref_id, $linkage_annotation,
$linkage_type, $ox_status, $unused_priority, $master_xref_id) || die "Could not insert object_xref data";
#ONLY add identity xref if object_xref was added successfully.
if( $insert_ox_sth->rows){
$added_count++;
$insert_ix_sth->execute($max_object_xref_id, $query_identity, $target_identity, $hit_start, $hit_end,
$translation_start, $translation_end, $cigar_line, $score, $evalue) || die "Could not insert identity_xref data";
}
else{
$ignored++;
}
}
}
}
print "Added $added_count new mapping but ignored $ignored\n";
if($tester->unlinked_entries){
die "Problems found after process_alt_alleles\n";
}
my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('alt_alleles_processed',now())");
$sth_stat->execute();
$sth_stat->finish;
}
#
# Copy the xrfs from the reference genes on to the alt alleles.
#
sub process_alt_alleles {
sub get_gene_specific_list {
my $self = shift;
#
# HGNC MGI and ZFIN_ID will already be done.
#
my @list = qw(DBASS3 DBASS5 EntrezGene miRBase RFAM UniGene Uniprot_genename WikiGene MIM_GENE MIM_MORBID);
return @list;
}
sub source_defined_move{
my $self = shift;
my $tester = XrefMapper::TestMappings->new($self);
if($tester->unlinked_entries){
die "Problems found before source_defined_move\n";
}
foreach my $source ($self->get_gene_specific_list()){
$self->biomart_fix($source,"Translation","Gene");
$self->biomart_fix($source,"Transcript","Gene");
}
if($tester->unlinked_entries){
die "Problems found after source_defined_move\n";
}
my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('source_level_move_finished',now())");
$sth_stat->execute();
$sth_stat->finish;
}
#sub process_alt_alleles {
# my $self = shift;
#
#
#
#
#
# my $sth_stat = $self->xref->dbc->prepare("insert into process_status (status, date) values('alt_alleles_processed',now())");
# $sth_stat->execute();
# $sth_stat->finish;
#}
1;
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