From 62ab49c206ba3a29d7e637a117d147d51e144c5a Mon Sep 17 00:00:00 2001
From: Andrew Yates <ayates@ebi.ac.uk>
Date: Fri, 27 Sep 2013 14:38:30 +0000
Subject: [PATCH] Making this script new alt allele compatible
---
misc-scripts/alt_alleles/alt_alleles.pl | 153 +++++++++++-------------
1 file changed, 72 insertions(+), 81 deletions(-)
diff --git a/misc-scripts/alt_alleles/alt_alleles.pl b/misc-scripts/alt_alleles/alt_alleles.pl
index 84a9204b1b..c171ad757a 100644
--- a/misc-scripts/alt_alleles/alt_alleles.pl
+++ b/misc-scripts/alt_alleles/alt_alleles.pl
@@ -1,7 +1,9 @@
#!/usr/bin/env perl
use strict;
+use warnings;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
+use Bio::EnsEMBL::AltAlleleGroup;
use Getopt::Long qw(:config pass_through);
# (make sure api version is correct
@@ -41,113 +43,102 @@ if(!defined($cdbname)){
}
#
-# Connect to the core database
+# Connect to the core & vega database
#
-my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $chost||'ens-staging1',
- -user => $cuser||'ensadmin',
- -pass => $cpass,
- -species => "test",
- -dbname => $cdbname||"homo_sapiens_core_63_37");
+my $core_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+ -host => $chost||'ens-staging1',
+ -user => $cuser||'ensadmin',
+ -pass => $cpass,
+ -group => 'core',
+ -dbname => $cdbname
+);
+my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
+ -host => $vhost||'ens-staging1',
+ -user => $vuser||'ensadmin',
+ -pass => $vpass,
+ -group => 'vega',
+ -dbname => $vdbname
+);
#
-# get ensembl gene ids and vega stable ids from the core database
+# get ensembl gene ids and vega stable ids from the *core* database
#
-
-
-my %vega_to_ens_id;
-my ($vega_stable_id, $gene_id);
-
-my $sth = $core_dba->dbc->prepare("select ensembl_id, display_label from object_xref join xref using(xref_id) join external_db using(external_db_id) where db_name = 'OTTG' and ensembl_object_type = 'Gene'");
-$sth->execute;
-
-$sth->bind_columns(\$gene_id, \$vega_stable_id);
-
-while ($sth->fetch){
- # sometimes we will see more than one gene associated with an OTTG
- # this happens when an OTTG on the primary assemby has been projected to a patch
- $vega_to_ens_id{$vega_stable_id}{$gene_id} = $gene_id;
-}
-$sth->finish;
-
-print "\nFetched ".(scalar(keys %vega_to_ens_id))." vega_stable_ids\n";
-
-my $vega_dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(-host => $vhost||'ens-staging1',
- -user => $vuser||'ensro',
- -port => $vport||3306,
- -dbname => $vdbname||"homo_sapiens_vega_63_37");
-
-#
-# SQL to get alt_allele data from vega
-#
-
-my $sql =(<<EOS);
-select aa.alt_allele_id, g.stable_id
- from alt_allele aa, gene g
- where aa.gene_id = g.gene_id
-EOS
-
-
-#
-# Store data in a hash where the key is the alt_id and the ensembl gene ids
-# stored in an anonymous array (value of the hash).
-#
-
-my $sth = $vega_dba->dbc->prepare($sql);
-$sth->execute;
-my ($alt_id, $vega_stable_id);
-my %alt_alleles;
-$sth->bind_columns(\$alt_id, \$vega_stable_id);
-
+my $vega_core_sql = <<'SQL';
+select ensembl_id, display_label
+from object_xref
+join xref using(xref_id)
+join external_db using(external_db_id)
+where db_name = 'OTTG'
+and ensembl_object_type = 'Gene'
+SQL
+
+# sometimes we will see more than one gene associated with an OTTG
+# this happens when an OTTG on the primary assemby has been projected to a patch.
+my %vega_to_ensembl_core_gene_id;
+$core_dba->dbc->sql_helper()->execute_no_return(-SQL => $vega_core_sql, -CALLBACK => sub {
+ my ($row) = @_;
+ my ($vega_stable_id, $gene_id) = @{$row};
+ $vega_to_ensembl_core_gene_id{$vega_stable_id}{$gene_id} = $gene_id;
+});
+
+print "\nFetched ".(scalar(keys %vega_to_ensembl_core_gene_id))." Vega Stable IDs\n";
+
+#
+# Get AltAlleles from vega
+#
+my $vega_aaga = $vega_dba->get_AltAlleleGroupAdaptor();
+#TODO deprecated call in 74
+my $vega_groups = $vega_aaga->fetch_all_Groups();
+# my $groups = $vega_aaga->fetch_all(); #replace the above with me ASAP
+
+my $cnt_vega_rows = @{$vega_groups};
+print STDERR "Fetched $cnt_vega_rows rows from the vega db alt_allele table\n";
my %no_gene_id;
-
-my $cnt_vega_rows = 0;
-while($sth->fetch()){
- $cnt_vega_rows++;
- if (exists $vega_to_ens_id{$vega_stable_id} ) {
- foreach my $gene_id ( keys %{$vega_to_ens_id{$vega_stable_id}} ) {
- push @{$alt_alleles{$alt_id}}, $gene_id ;
+my @new_groups;
+foreach my $group (@{$vega_groups}) {
+ my $members = $group->get_all_Genes_types();
+ my $new_core_group = undef;
+ foreach my $member (@{$members}) {
+ my ($vega_gene, $attribs_hash) = @{$member};
+ if(exists $vega_to_ensembl_core_gene_id{$vega_gene->stable_id()}) {
+ $new_core_group ||= Bio::EnsEMBL::AltAlleleGroup->new(); # initalise if we don't already have one
+ foreach my $gene_id (keys %{$vega_to_ens_id{$vega_stable_id}} ) {
+ #Add each gene in. If we had a 1:m relationship then we copy the attribute already assigned
+ #across
+ $new_core_group->add_member($gene_id, $attribs_hash);
+ }
+ }
+ else {
+ push @{$no_gene_id{$group->dbID()}}, $vega_stable_id;
+ print STDERR "no ensembl gene_id found for vega stable id $vega_stable_id in core\n";
}
- } else {
- push @{$no_gene_id{$alt_id}}, $vega_stable_id;
- print STDERR "no ensembl gene_id found for vega stable id $vega_stable_id in core\n";
}
+ push(@new_groups, $new_core_group);
}
-$sth->finish;
-print STDERR "Fetched $cnt_vega_rows rows from the vega db alt_allele table\n";
#
# Delete the old data
#
-
print STDERR "\n\nDeleting all alt_alleles...\n\n";
-my $sth = $core_dba->dbc->prepare("delete from alt_allele");
-$sth->execute;
+$core_dba->dbc->do("delete from alt_allele");
#
# Store alt_alleles.
#
-
print STDERR "Storing new alt alleles...\n\n";
my $alt_allele_count=0;
my $gene_count = 0;
-my $ga = $core_dba->get_adaptor("gene");
-
-foreach my $key (keys %alt_alleles){
- my @gene_ids = @{$alt_alleles{$key}};
- my @genes;
- foreach my $gene_id (@gene_ids) {
- push @genes, $ga->fetch_by_dbID($gene_id);
- }
-
- my $alt_allele_id = $ga->store_alt_alleles(\@genes);
- $alt_allele_count ++ if ($alt_allele_id);
- $gene_count += scalar(@genes) if ($alt_allele_id);
+my $core_aaga = $core_dba->get_AltAlleleGroupAdaptor();
+foreach my $group (@new_groups) {
+ my $alt_allele_id = $core_aaga->store($group);
+ $alt_allele_count++;
+ $gene_count += $group->size()
}
print "Added $alt_allele_count alt_allele ids for $gene_count genes\nDONE\n";
--
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