From 7f161c1e23350d5a69e0907c4a4e1faa8c9994a6 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 9 Jan 2012 15:19:59 +0000
Subject: [PATCH] Store Clone_based_ensembl_gene descriptions last, to avoid an
accession name conflict with Clone_based_vega_gene descriptions. Assign an
HGNC name which hasn't been used if possible.
---
.../xref_mapping/XrefMapper/OfficialNaming.pm | 140 +++++++++++++-----
1 file changed, 102 insertions(+), 38 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
index efd2dcd726..ca26fb1ada 100644
--- a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
@@ -191,7 +191,10 @@ SQ0
my %xref_added; # store those added $xref_added{$accession:$source_id} = $xref_id;
my %seen_gene;
- foreach my $gene_id (@sorted_gene_ids){
+ my %ens_clone_genes;
+ my %official_name_used;
+
+ while ( my $gene_id = shift @sorted_gene_ids){
my $tran_source = $dbname;
@@ -213,6 +216,8 @@ SQ0
cbvt => $dbname_to_source_id->{"Clone_based_vega_transcript"}
});
+ if (!defined($ens_clone_genes{$gene_id})) { #we're processing this gene for the first time
+
################################
# Get offical name if it has one
################################
@@ -220,7 +225,13 @@ SQ0
$self->get_official_domain_name({gene_id => $gene_id,
gene_to_tran => \%gene_to_transcripts,
tran_to_vega_name => $tran_to_vega_name,
- gene_id_to_stable_id => \%gene_id_to_stable_id});
+ gene_id_to_stable_id => \%gene_id_to_stable_id,
+ official_name_used => \%official_name_used
+ });
+
+ if (defined($gene_symbol_xref_id)) {
+ $official_name_used{$gene_symbol_xref_id} = 1;
+ }
############################################
# If not found see if there is an LRG entry
@@ -252,6 +263,8 @@ SQ0
}
}
+ } #if (!exists($ens_clone_genes{$gene_id}))
+
##############################################
# Finally if all else fails use the clone name
##############################################
@@ -271,7 +284,7 @@ SQ0
next;
}
- if(defined($gene_symbol)){
+ if(defined($gene_symbol) && !defined($ens_clone_genes{$gene_id})){
my $desc = $display_label_to_desc{$gene_symbol};
if(!defined($gene_symbol_xref_id)){
@@ -292,11 +305,14 @@ SQ0
xref_added => \%xref_added,
seen_gene => \%seen_gene,
gene_to_tran => \%gene_to_transcripts,
- tran_to_vega_ext => $tran_to_vega_ext });
+ tran_to_vega_ext => $tran_to_vega_ext,
+ ens_clone_genes => \%ens_clone_genes,
+ });
}
- else{ # use clone name
- $self->set_transcript_and_gene_display_xref_via_clone_name({vega_clone_name => $vega_clone_name,
+ if (!defined($gene_symbol)) { # use clone name
+
+ my $keep_gene = $self->set_transcript_and_gene_display_xref_via_clone_name({vega_clone_name => $vega_clone_name,
clone_name => $clone_name,
dbname_to_source => $dbname_to_source_id,
gene_id => $gene_id,
@@ -304,8 +320,12 @@ SQ0
max_object => \$max_object_xref_id,
xref_added => \%xref_added,
gene_to_tran => \%gene_to_transcripts,
- tran_to_vega_ext => $tran_to_vega_ext
+ tran_to_vega_ext => $tran_to_vega_ext,
+ ens_clone_genes => \%ens_clone_genes,
});
+ if ($keep_gene) {
+ push @sorted_gene_ids, $gene_id;
+ }
}
} # for each gene
@@ -344,6 +364,7 @@ sub get_official_domain_name{
my $gene_id_to_stable_id = $arg_ref->{gene_id_to_stable_id};
my $tran_to_vega_name = $arg_ref->{tran_to_vega_name};
my $gene_to_transcripts = $arg_ref->{gene_to_tran};
+ my $official_name_used = $arg_ref->{official_name_used};
my $dbname = $self->get_official_name();
@@ -424,6 +445,9 @@ sub get_official_domain_name{
$best_list{$xref_id_to_display{$xref_id}} = 1;
}
+ #print "Multiple best ".$dbname."'s using vega gene description to find the best name for ".$gene_id_to_stable_id->{$gene_id}."\n";
+ #add this section when OTTG xrefs have gene name in description
+
my %name_count;
foreach my $tran_id (@{$gene_to_transcripts->{$gene_id}}){
if(defined($tran_to_vega_name->{$tran_id}) and defined($best_list{$tran_to_vega_name->{$tran_id}})){
@@ -441,9 +465,9 @@ sub get_official_domain_name{
$gene_symbol = $name;
}
}
- foreach my $xref_id (keys %ODN){
- if($gene_symbol eq $xref_id_to_display{$xref_id}){
- $gene_symbol_xref_id = $xref_id;
+ foreach my $x (keys %ODN){
+ if($gene_symbol eq $xref_id_to_display{$x}){
+ $gene_symbol_xref_id = $x;
}
}
print "\t$gene_symbol chosen from vega\n";
@@ -461,19 +485,43 @@ sub get_official_domain_name{
}
}
- # take the first one ??
- my $i = 0;
+ # take the name which hasn't been already assigned to another gene, if possible
+
+ my $xref_not_used;
foreach my $x (keys %ODN){
- print "\t".$xref_id_to_display{$x};
- if(!$i){
- print " (chosen as first)\n";
- $gene_symbol = $xref_id_to_display{$x};
- $gene_symbol_xref_id = $x;
- }
- else{
- print " (left as $dbname reference but not gene symbol)\n";
- }
- $i++;
+ if (!defined($official_name_used->{$x}) ) {
+ $xref_not_used = $x;
+ }
+ }
+ if ($xref_not_used) {
+ foreach my $x (keys %ODN){
+ print "\t".$xref_id_to_display{$x};
+ if ($x == $xref_not_used) {
+ print " chosen\n";
+ $gene_symbol = $xref_id_to_display{$x};
+ $gene_symbol_xref_id = $x;
+ } else {
+ print " (left as $dbname reference but not gene symbol)\n";
+ }
+ }
+
+ } else {
+
+ my $i=0;
+ foreach my $x (keys %ODN){
+ print "\t".$xref_id_to_display{$x};
+ if(!$i){
+ print " (chosen as first)\n";
+ $gene_symbol = $xref_id_to_display{$x};
+ $gene_symbol_xref_id = $x;
+ }
+ else{
+ print " (left as $dbname reference but not gene symbol)\n";
+ }
+ $i++;
+ }
+
+
}
}
}
@@ -495,6 +543,7 @@ sub set_transcript_and_gene_display_xref_via_clone_name{
my $tran_to_vega_ext = $arg_ref->{tran_to_vega_ext};
my $vega_clone_name = $arg_ref->{vega_clone_name};
my $clone_name = $arg_ref->{clone_name};
+ my $ens_clone_names = $arg_ref->{ens_clone_genes};
my $ins_xref_sth = $self->get_ins_xref_sth();
my $ins_dep_ix_sth = $self->get_ins_dep_ix_sth();
@@ -502,35 +551,50 @@ sub set_transcript_and_gene_display_xref_via_clone_name{
my $ins_object_xref_sth = $self->get_ins_object_xref_sth();
my $set_gene_display_xref_sth = $self->get_set_gene_display_xref_sth();
+ my $keep_gene;
my $t_source_id;
my $g_source_id;
my $desc;
my $name;
- if(defined($vega_clone_name)){
+ if(defined($vega_clone_name) && !defined($ens_clone_names->{$gene_id})){
$name = $vega_clone_name;
$t_source_id = $dbname_to_source_id->{"Clone_based_vega_transcript"};
$g_source_id = $dbname_to_source_id->{"Clone_based_vega_gene"};
+ $name = $vega_clone_name;
$desc = "via havana clone name";
- }
- else{
- if(defined($clone_name)){
- $name = $clone_name;
- $t_source_id = $dbname_to_source_id->{"Clone_based_ensembl_transcript"};
- $g_source_id = $dbname_to_source_id->{"Clone_based_ensembl_gene"};
- $desc = "via ensembl clone name";
- }
- else{
- croak "No name";
- }
my $num = 1;
my $unique_name = $name.".".$num;
- while(defined($xref_added->{$unique_name.":".$g_source_id})){
- $num++;
- $unique_name = $name.".".$num;
+ while(defined($xref_added->{$unique_name.":".$g_source_id}) ){
+ $num++;
+ $unique_name = $name.".".$num;
}
$name = $unique_name;
}
+ if (!defined($vega_clone_name) ) {
+ if (defined($ens_clone_names->{$gene_id})) {
+ if(defined($clone_name)){
+ $name = $clone_name;
+ $t_source_id = $dbname_to_source_id->{"Clone_based_ensembl_transcript"};
+ $g_source_id = $dbname_to_source_id->{"Clone_based_ensembl_gene"};
+ $desc = "via ensembl clone name";
+ }
+ else{
+ croak "No name";
+ }
+ my $num = 1;
+ my $unique_name = $name.".".$num;
+ while(defined($xref_added->{$unique_name.":".$g_source_id}) || defined($xref_added->{$unique_name.":".$dbname_to_source_id->{"Clone_based_vega_gene"}})){
+ $num++;
+ $unique_name = $name.".".$num;
+ }
+ $name = $unique_name;
+ } else {
+ $ens_clone_names->{$gene_id} = 1;
+ $keep_gene = 1;
+ return $keep_gene;
+ }
+ }
# first add the gene xref and set display_xref_id
# store the data
@@ -579,7 +643,7 @@ sub set_transcript_and_gene_display_xref_via_clone_name{
$set_tran_display_xref_sth->execute($$max_xref_id, $tran_id);
}
}
- return;
+ return 0;
}
###########################################################
--
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