From 9bdbb41e3d950e9e979991e6223f5adc93f80ec2 Mon Sep 17 00:00:00 2001
From: Ian Longden <ianl@sanger.ac.uk>
Date: Mon, 5 Sep 2011 15:35:38 +0000
Subject: [PATCH] More docs added
---
.../xref_mapping/XrefMapper/OfficialNaming.pm | 208 +++++++++++++-----
1 file changed, 148 insertions(+), 60 deletions(-)
diff --git a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
index 57008201d8..01a6dfaa39 100644
--- a/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
+++ b/misc-scripts/xref_mapping/XrefMapper/OfficialNaming.pm
@@ -51,6 +51,11 @@ use base qw( XrefMapper::BasicMapper);
#
##############################################################################################
+
+####################################
+# Create OfficialNaming object
+# Get some info from the BasicMapper
+####################################
sub new {
my($class, $mapper) = @_;
@@ -66,6 +71,11 @@ sub new {
return $self;
}
+
+##################################################
+# This will be the offical database name
+# HGNC, MGI or ZFIN_ID, comes from BasicMapper
+#################################################
sub get_official_name {
my ($self, $arg) = @_;
@@ -74,6 +84,11 @@ sub get_official_name {
return $self->{_official_name};
}
+
+
+##################################################
+# This is the main subroutine that does everything
+##################################################
sub run {
my $self = shift;
@@ -117,10 +132,8 @@ sub run {
######################################################
my ($max_object_xref_id, $max_xref_id) = $self->find_max_ids();
-
- my %display_label_to_id;
my %display_label_to_desc;
- $self->get_display_label_data(\%display_label_to_id,\%display_label_to_desc);
+ $self->get_display_label_data(\%display_label_to_desc);
my %synonym;
$self->get_synonyms(\%synonym);
@@ -192,6 +205,9 @@ SQ0
my $vega_clone_name = undef;
my $clone_name = undef;
+ ########################################
+ # Get the vega data needed for this gene
+ ########################################
my ($tran_to_vega_ext, $tran_to_vega_name, $tran_to_vega_xref_id) =
$self->get_tran_to_vega_data({ gene_id => $gene_id,
gene_to_tran => \%gene_to_transcripts,
@@ -201,20 +217,36 @@ SQ0
cbvt => $dbname_to_source_id->{"Clone_based_vega_transcript"}
});
- ($gene_symbol, $gene_symbol_xref_id) = $self->get_official_domain_name({gene_id => $gene_id,
- gene_to_tran => \%gene_to_transcripts,
- tran_to_vega_name => $tran_to_vega_name,
- gene_id_to_stable_id => \%gene_id_to_stable_id});
-
+ ################################
+ # Get offical name if it has one
+ ################################
+ ($gene_symbol, $gene_symbol_xref_id) =
+ $self->get_official_domain_name({gene_id => $gene_id,
+ gene_to_tran => \%gene_to_transcripts,
+ tran_to_vega_name => $tran_to_vega_name,
+ gene_id_to_stable_id => \%gene_id_to_stable_id});
+
+ ############################################
+ # If not found see if there is an LRG entry
+ ############################################
if(!defined($gene_symbol)){ # look for LRG
($gene_symbol, $gene_symbol_xref_id) = $self->find_lrg_hgnc($gene_id);
}
- if(!defined($gene_symbol)){ # try the other database source (should be RFAM and miRBase only)
- ($gene_symbol, $gene_symbol_xref_id) = $self->find_from_other_sources({gene_id => $gene_id,
- tran_source => \$tran_source});
+ ####################################################
+ # If not found look for other valid database sources
+ # At present RFAm and miRBase are the only ones.
+ ####################################################
+ if(!defined($gene_symbol)){
+ ($gene_symbol, $gene_symbol_xref_id) =
+ $self->find_from_other_sources({gene_id => $gene_id,
+ label_to_desc => \%display_label_to_desc,
+ tran_source => \$tran_source});
}
+ ###################################################
+ # If still no joy see if there is a vega clone name
+ ###################################################
if(!defined($gene_symbol)){
foreach my $tran_id (@{$gene_to_transcripts{$gene_id}}){
my $source_id = $dbname_to_source_id->{"Clone_based_vega_transcript"};
@@ -224,26 +256,26 @@ SQ0
}
}
- if(!defined($gene_symbol) ){ # No HGNC or other so look for vega clone names
- if(!defined($vega_clone_name)){ #if no vega clone name use the ensembl clone name
- $clone_name = $self->get_clone_name($gene_id, $ga, $dbname);
- if(defined($clone_name)){
- $clone_name =~ s/[.]\d+//; #remove .number
- }
+ ##############################################
+ # Finally if all else fails use the clone name
+ ##############################################
+ if((!defined($gene_symbol)) and (!defined($vega_clone_name))){
+ $clone_name = $self->get_clone_name($gene_id, $ga, $dbname);
+ if(defined($clone_name)){
+ $clone_name =~ s/[.]\d+//; #remove .number
}
}
- #
+ ######################################
# Check we have a suitable name to use.
- #
+ # Else give error message and goto next
+ ######################################
if( !(defined($clone_name) or defined($vega_clone_name) or defined($gene_symbol)) ){
carp "Problem gene ".$gene_id_to_stable_id{$gene_id}." could not get a clone name or ".$dbname." symbol\n";
next;
}
if(defined($gene_symbol)){
- #gene symbol already set as it is HGNC or MGI so do not need add a new xref anything for the gene;
-
my $desc = $display_label_to_desc{$gene_symbol};
if(!defined($gene_symbol_xref_id)){
@@ -294,6 +326,21 @@ SQ0
return;
}
+
+
+
+####################################################################
+# Get offical name if it has one
+#
+# Search gene for dbname entries.
+# dbname (HGNC||MGI||ZFIN_ID depenedent on species
+#
+# Find the "best" one
+# Remove the lesser ones (set status to MULTI_DELETE for object_xref)
+#
+# returns the gene_symbol and xref_id of the best one
+######################################################################
+
sub get_official_domain_name{
my ($self, $arg_ref) = @_;
@@ -353,20 +400,6 @@ sub get_official_domain_name{
}
if(scalar(@ODN) > 1){ # try to use vega to find the most common one
- if($gene_id_to_stable_id->{$gene_id} eq "ENSG00000213030"){ #start debug
- print "----ODN\n";
- foreach my $xref_id (@ODN){
- print "---\t".$xref_id."\t".$xref_id_to_display{$xref_id}."\n";
- }
- foreach my $tran_id (@{$gene_to_transcripts->{$gene_id}}){
- print "--".$tran_id;
- if(defined($tran_to_vega_name->{$tran_id})){
- print "\t".$tran_to_vega_name->{$tran_id};
- }
- print "\n";
- }
- } ## end debug
-
my %best_list;
foreach my $xref_id (@ODN){
$best_list{$xref_id_to_display{$xref_id}} = 1;
@@ -517,10 +550,15 @@ sub set_transcript_and_gene_display_xref_via_clone_name{
return;
}
-
+###########################################################
+# Set the transcript display xrefs
+#
+# Use the gene symbol to create a transcript display xref
+# Add the Vega ext if it exists else start at 201 and
+# increment.
+###########################################################
sub set_transcript_display_xrefs{
my ($self, $arg_ref) = @_;
-# my ($self, $max_xref_id, $max_object_xref_id, $gene_id, $gene_symbol, $desc, $source_id, $xref_added, $seen_gene, $gene_to_transcripts, $tran_to_vega_ext) = @_;
my $max_xref_id = $arg_ref->{max_xref};
my $max_object_xref_id = $arg_ref->{max_object};
@@ -533,21 +571,21 @@ sub set_transcript_display_xrefs{
my $gene_to_transcripts = $arg_ref->{gene_to_tran};
my $tran_to_vega_ext = $arg_ref->{tran_to_vega_ext};
-# croak ("MISSING parameters for set_transcript_display_xrefs")
-# if any (!defined($_)) $max_xref_id, $max_object_xref_id, $gene_id, $gene_symbol, $desc, $source_id, $xref_added, $seen_gene, $gene_to_transcripts, $tran_to_vega_ext;
+ # statement handles needed
my $ins_xref_sth = $self->get_ins_xref_sth();
my $ins_dep_ix_sth = $self->get_ins_dep_ix_sth();
my $set_tran_display_xref_sth = $self->get_set_transcript_display_xref_sth();
my $ins_object_xref_sth = $self->get_ins_object_xref_sth();
+
my $no_vega_ext = 201;
if(defined($seen_gene->{$gene_symbol})){
$no_vega_ext = $seen_gene->{$gene_symbol};
}
+
foreach my $tran_id ( @{$gene_to_transcripts->{$gene_id}} ){
my $ext;
-# my $source_id = $dbname_to_source_id->($tran_source);
if(defined($tran_to_vega_ext->{$tran_id})){
$ext = $tran_to_vega_ext->{$tran_id};
}
@@ -573,6 +611,12 @@ sub set_transcript_display_xrefs{
return;
}
+
+#################################################
+# Get statement handle to retrieve what xrefs
+# are attached to a specific ensembl_id and type
+# for a particular source name
+#################################################
sub get_dbentrie_sth{
my $self = shift;
@@ -593,7 +637,36 @@ SQ1
return $self->{'_dbentrie_sth'};
}
+#################################################
+# Get statement handle to retrieve what xrefs
+# are attached to a specific ensembl_id and type
+# for a particular source name with description
+#################################################
+sub get_dbentrie_with_desc_sth{
+ my $self = shift;
+
+ if(!defined($self->{'_dbentrie_desc_sth'})){
+ my $sql =(<<"SQD");
+SELECT x.label, x.xref_id, ox.object_xref_id, s.prioriy, x.description
+ FROM xref x, object_xref ox, source s
+ WHERE x.xref_id = ox.xref_id AND
+ x.source_id = s.source_id AND
+ s.name = ? AND
+ ox.ox_status = 'DUMP_OUT' AND
+ ox.ensembl_id = ? AND
+ ox.ensembl_object_type = ?
+SQD
+ $self->{'_dbentrie_desc_sth'} = $self->xref->dbc->prepare($sql);
+ }
+ return $self->{'_dbentrie_desc_sth'};
+}
+
+#################################################
+# Get statement handle to set the display xref
+# for a transcript in the xref database.
+# Stored in the transcript_stable_id table.
+#################################################
sub get_set_transcript_display_xref_sth {
my $self = shift;
if(!defined($self->{'_set_tran_display'})){
@@ -602,6 +675,12 @@ sub get_set_transcript_display_xref_sth {
return $self->{'_set_tran_display'}
}
+
+#################################################
+# Get statement handle to set the display xref
+# for a gene in the xref database.
+# Stored in the gene_stable_id table.
+#################################################
sub get_set_gene_display_xref_sth {
my $self = shift;
if(!defined($self->{'_set_gene_display'})){
@@ -611,6 +690,9 @@ sub get_set_gene_display_xref_sth {
}
+###############################################
+# Get statement handle to insert an xref
+###############################################
sub get_ins_xref_sth{
my $self= shift;
@@ -622,6 +704,10 @@ sub get_ins_xref_sth{
return $self->{'_ins_xref_sth'};
}
+
+#################################################
+# Get statement handle to insert an identity xref
+#################################################
sub get_ins_dep_ix_sth{
my $self= shift;
@@ -632,6 +718,9 @@ sub get_ins_dep_ix_sth{
return $self->{'_ins_identity_sth'};
}
+###############################################
+# Get statement handle to insert an object_xref
+###############################################
sub get_ins_object_xref_sth{
my $self= shift;
@@ -671,16 +760,15 @@ sub find_max_ids{
return $max_object_xref_id, $max_xref_id;
}
+
+
sub get_tran_to_vega_data{
-# my ($self, $gene_id, $ref_gene_to_transcripts, $ref_display_label_to_desc, $ref_synonym, $ref_best_list, $ref_name_count) = @_;
my ($self, $arg_ref) = @_;
my $gene_id = $arg_ref->{gene_id};
my $ref_gene_to_transcripts = $arg_ref->{gene_to_tran};
my $ref_display_label_to_desc = $arg_ref->{label_to_desc};
my $ref_synonym = $arg_ref->{synonym};
- my $ref_best_list = $arg_ref->{best_list};
- my $ref_name_count = $arg_ref->{name_count};
my $ref_xref_added = $arg_ref->{xref_added};
my $clone_based_vega_transcript_id = $arg_ref->{cbvt};
@@ -728,9 +816,10 @@ sub get_tran_to_vega_data{
if( (!defined($num)) or (!$num) or ($num eq "")){
print "Problem finding number for $display\n";
}
-
+
+ $tran_to_vega_name{$tran_id} = $symbol_bit;
$tran_to_vega_ext{$tran_id} = $num;
-
+
if(defined($ref_display_label_to_desc->{$symbol_bit})){
}
elsif(defined($ref_synonym->{$symbol_bit})){
@@ -745,9 +834,6 @@ sub get_tran_to_vega_data{
next;
}
}
-# if($ref_best_list->{$symbol_bit}){
-# $ref_name_count->{$symbol_bit}++;
-# }
}
}
return \%tran_to_vega_ext,\%tran_to_vega_name, \%tran_to_vega_xref_id;
@@ -779,7 +865,8 @@ SYN
}
sub get_display_label_data{
- my ($self, $label_to_id, $label_to_desc) = @_;
+# my ($self, $label_to_id, $label_to_desc) = @_;
+ my ($self, $label_to_desc) = @_;
my $dbname = $self->get_official_name();
@@ -797,7 +884,7 @@ GD1
my ($display_label, $acc, $syn, $desc);
$gd1_sth->bind_columns(\$acc,\$display_label, \$desc);
while($gd1_sth->fetch){
- $label_to_id->{$display_label} = $acc;
+# $label_to_id->{$display_label} = $acc;
$label_to_desc->{$display_label} = $desc;
}
$gd1_sth->finish;
@@ -817,7 +904,7 @@ GD2
$gd2_sth->execute();
$gd2_sth->bind_columns(\$acc,\$display_label, \$desc);
while($gd2_sth->fetch){
- $label_to_id->{$display_label} = $acc;
+# $label_to_id->{$display_label} = $acc;
if(!defined($desc)){
warn "undef desc for $display_label\n";
}
@@ -839,27 +926,31 @@ sub get_other_name_hash{
return $self->{'_other_name'};
}
+
+
+
sub find_from_other_sources{
my ($self, $ref_args) = @_;
- my $tran_source = $ref_args->{tran_source};
- my $gene_id = $ref_args->{gene_id};
-
+ my $tran_source = $ref_args->{tran_source};
+ my $gene_id = $ref_args->{gene_id};
+ my $display_label_to_desc = $ref_args->{label_to_desc};
my ($gene_symbol, $gene_symbol_xref_id);
- my $dbentrie_sth = $self->get_dbentrie_sth();
+ my $dbentrie_sth = $self->get_dbentrie_with_desc_sth();
my $other_name_num = $self->get_other_name_hash();
- my ($display, $xref_id, $object_xref_id, $level);
+ my ($display, $xref_id, $object_xref_id, $level, $desc);
foreach my $ext_db_name (qw(miRBase RFAM)){
$dbentrie_sth->execute($ext_db_name, $gene_id, "Gene");
- $dbentrie_sth->bind_columns(\$display, \$xref_id, \$object_xref_id, \$level);
+ $dbentrie_sth->bind_columns(\$display, \$xref_id, \$object_xref_id, \$level, \$desc);
while($dbentrie_sth->fetch){
$gene_symbol = $display;
$gene_symbol_xref_id = $xref_id;
$$tran_source = $ext_db_name;
+ $display_label_to_desc->{$display} = $desc;
if(defined($other_name_num->{$gene_symbol})){
$other_name_num->{$gene_symbol}++;
}
@@ -890,9 +981,6 @@ sub get_delete_odn_sth{
sub set_the_best_odn{
my ($self, $odn, $ref_list, $ref_list_ox, $ref_xref_id_to_display) = @_;
-# my @list = @{$ref_list};
-# my @list_ox = @{$ref_list_ox};
-
my $delete_odn_sth = $self->get_delete_odn_sth();
--
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