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Commit aef7bd10 authored by Magali Ruffier's avatar Magali Ruffier
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HGNC header format has changed, so we update the parser to cope with it 

given the file has custom chosen columns, we decide to refer to them according
to the order in which they are given, rather than through their header name
which might change
parent 9d5742db
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misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+ 106
− 94
View file @ aef7bd10
......@@ -41,8 +41,10 @@ sub run {
return 1;
}
my ($name_to_source_id, $name_to_array_index)
= $self->process_header($hugo_io->getline());
my $name_to_source_id = $self->get_hgnc_sources();
# Skip header
$hugo_io->getline();
while ( $_ = $hugo_io->getline() ) {
chomp;
......@@ -50,15 +52,15 @@ sub run {
my $seen = 0;
my $acc = $array[$name_to_array_index->{'desc_only'}];
my $symbol = $array[$name_to_array_index->{'Approved Symbol'}];
my $name = $array[$name_to_array_index->{'Approved Name'}];
my $previous_symbols = $array[$name_to_array_index->{'Previous Symbols'}];
my $synonyms = $array[$name_to_array_index->{'Synonyms'}];
my $acc = $array[0];
my $symbol = $array[1];
my $name = $array[2];
my $previous_symbols = $array[3];
my $synonyms = $array[4];
my $type = 'Locus Specific Databases';
my $id = $array[$name_to_array_index->{$type}];
my $type = 'lrg';
my $id = $array[11];
my $source_id = $name_to_source_id->{$type};
if($id and $id =~ m/http:\/\/www.lrg-sequence.org\/LRG\/(LRG_\d+)/x){
my $lrg_stable_id = $1;
......@@ -83,7 +85,7 @@ sub run {
# Direct Ensembl mappings
#
$type = 'ensembl_manual';
$id = $array[$name_to_array_index->{$type}];
$id = $array[9];
$source_id = $name_to_source_id->{$type};
if ($id){ # Ensembl direct xref
$seen = 1;
......@@ -107,27 +109,49 @@ sub run {
#
# RefSeq
#
foreach my $type (qw(refseq_mapped refseq_manual)){
$id = $array[$name_to_array_index->{$type}];
$source_id = $name_to_source_id->{$type};
if ($id) {
if(defined $refseq{$id} ){
$seen = 1;
foreach my $xref_id (@{$refseq{$id}}){
$name_count{$type}++;
$self->add_dependent_xref({ master_xref_id => $xref_id,
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
}
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
$type = 'refseq_mapped';
$id = $array[8];
$source_id = $name_to_source_id->{$type};
if ($id) {
if(defined $refseq{$id} ){
$seen = 1;
foreach my $xref_id (@{$refseq{$id}}){
$name_count{$type}++;
$self->add_dependent_xref({ master_xref_id => $xref_id,
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
}
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
}
}
$type = 'refseq_manual';
$id = $array[6];
$source_id = $name_to_source_id->{$type};
if ($id) {
if(defined $refseq{$id} ){
$seen = 1;
foreach my $xref_id (@{$refseq{$id}}){
$name_count{$type}++;
$self->add_dependent_xref({ master_xref_id => $xref_id,
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
}
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
}
}
......@@ -135,7 +159,7 @@ sub run {
# Swissprot
#
$type = 'swissprot_manual';
$id = $array[$name_to_array_index->{$type}];
$id = $array[10];
$source_id = $name_to_source_id->{$type};
if ($id) { # Swissprot
if(defined $swissprot{$id} ){
......@@ -161,29 +185,49 @@ sub run {
#
# EntrezGene
#
foreach my $type (qw(entrezgene_manual entrezgene_mapped)){
$id = $array[$name_to_array_index->{$type}];
$source_id = $name_to_source_id->{$type};
if(defined $id ){
if(defined $entrezgene{$id} ){
$seen = 1;
$self->add_dependent_xref({ master_xref_id => $entrezgene{$id},
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
$name_count{$type}++;
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
}
$type = 'entrezgene_manual';
$id = $array[5];
$source_id = $name_to_source_id->{$type};
if(defined $id ){
if(defined $entrezgene{$id} ){
$seen = 1;
$self->add_dependent_xref({ master_xref_id => $entrezgene{$id},
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
$name_count{$type}++;
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
}
}
$type = 'entrezgene_mapped';
$id = $array[7];
if(defined $id ){
if(defined $entrezgene{$id} ){
$seen = 1;
$self->add_dependent_xref({ master_xref_id => $entrezgene{$id},
acc => $acc,
label => $symbol,
desc => $name || '',
source_id => $source_id,
species_id => $species_id} );
$name_count{$type}++;
$self->add_synonyms_for_hgnc( {source_id => $source_id,
name => $acc,
species_id => $species_id,
dead => $previous_symbols,
alias => $synonyms});
}
}
if(!$seen){ # Store to keep descriptions etc
$type = 'desc_only';
$source_id = $name_to_source_id->{$type};
......@@ -218,60 +262,28 @@ sub run {
sub process_header{
sub get_hgnc_sources {
my $self = shift;
my $header = shift;
my %name_to_source_id;
my %name_to_array_index;
my %header_to_name = ( 'HGNC ID' => 'desc_only',
'Approved Symbol' => 0,
'Approved Name' => 0,
'Previous Symbols' => 0,
'Synonyms' => 0,
'Entrez Gene ID' => 'entrezgene_manual',
'RefSeq IDs' => 'refseq_manual',
'Entrez Gene ID ' => 'entrezgene_mapped', #note space needed
'RefSeq ' => 'refseq_mapped',
'Ensembl Gene ID' => 'ensembl_manual',
'UniProt ID ' => 'swissprot_manual',
'Locus Specific Databases' => 0);
foreach my $key (keys %header_to_name){
if($header_to_name{$key}){
my $source_id =
$self->get_source_id_for_source_name('HGNC',$header_to_name{$key});
if(!(defined $source_id)){
die 'Could not get source id for '.$header_to_name{$key}."\n";
}
$name_to_source_id{ $header_to_name{$key} } = $source_id;
my @sources = ('entrezgene_manual', 'refseq_manual', 'entrezgene_mapped', 'refseq_mapped', 'ensembl_manual', 'swissprot_manual', 'desc_only');
foreach my $key (@sources) {
my $source_id = $self->get_source_id_for_source_name('HGNC', $key);
if(!(defined $source_id)){
die 'Could not get source id for HGNC and '. $key ."\n";
}
$name_to_source_id{ $key } = $source_id;
}
my $source_id = $self->get_source_id_for_source_name('LRG_HGNC_notransfer');
if(!(defined $source_id) ){
die 'Could not get source id for LRG_HGNC_notransfer\n';
}
$name_to_source_id{'Locus Specific Databases'} = $source_id;
chomp $header;
my @items = split /\t/x, $header;
my $i=0;
foreach my $h (@items){
$h =~ s/\(.*\)//x;
if((defined $header_to_name{$h}) and $header_to_name{$h}){
$name_to_array_index{$header_to_name{$h}} = $i++;
}
elsif(defined $header_to_name{$h}){
$name_to_array_index{$h} = $i++;
}
else{
die "Problem with $h not listed\n";
}
}
$name_to_source_id{'lrg'} = $source_id;
return \%name_to_source_id, \%name_to_array_index;
return \%name_to_source_id;
}
sub add_synonyms_for_hgnc{
......
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