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Commit 4f8506fc authored by Ian Longden's avatar Ian Longden
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made addition of synonyms a method instead of multiple lines all the same

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misc-scripts/xref_mapping/XrefParser/HGNCParser.pm
+ 58
− 88
View file @ 4f8506fc
......@@ -72,6 +72,11 @@ sub run {
my $hgnc_desc_only = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","desc_only");
if(!defined($hgnc_desc_only)){
die "Could not get source id for HGNC with priority description of desc_only\n";
}
my $hgnc_lrg = XrefParser::BaseParser->get_source_id_for_source_name("LRG_HGNC_notransfer");
if(!defined($hgnc_lrg)){
die "Could not get source id for LRG_HGNC_notransfer\n";
}
my (%swissprot) = %{XrefParser::BaseParser->get_valid_codes("Uniprot/SWISSPROT",$species_id)};
......@@ -111,6 +116,7 @@ sub run {
# 8 RefSeq ID mapped
# 9 Ensembl ID manual
#10 Swissprot ID manual
#11 <strong>.....</strong> look for lrg specification
my @array = split(/\t/,$_);
......@@ -118,24 +124,21 @@ sub run {
# If no RefSeq, use the Swissprot instead
my $seen = 0;
if($array[11] and $array[11] =~ /http:\/\/www.lrg-sequence.org\/LRG\/(LRG_\d+)\'/){
# print $array[0]." linked to LRG $1\n";
my $lrg_stable_id = $1;
XrefParser::BaseParser->add_to_direct_xrefs($lrg_stable_id, 'gene', $array[0], '', $array[1], $array[2], "", $hgnc_lrg, $species_id);
$self->add_synonyms_for_hgnc($hgnc_lrg, $array[0], $species_id, $array[3], $array[4]);
}
if ($array[9]){ # Ensembl direct xref
$seen =1;
$seen = 1;
$ensembl_count++;
XrefParser::BaseParser->add_to_direct_xrefs($array[9],'gene', $array[0], '', $array[1], $array[2], "", $hgnc_ensembl_mapped, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_ensembl_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_ensembl_mapped, $arr, $species_id);
}
}
$self->add_synonyms_for_hgnc($hgnc_ensembl_mapped, $array[0], $species_id, $array[3], $array[4]);
}
if ($array[6]) { # RefSeq
......@@ -143,125 +146,92 @@ sub run {
$seen = 1;
$refseq_count++;
XrefParser::BaseParser->add_to_xrefs($refseq{$array[6]}, $array[0], '', $array[1], $array[2], "", $hgnc_refseq_manual, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_manual, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_manual, $arr, $species_id);
}
}
}
$self->add_synonyms_for_hgnc($hgnc_refseq_manual, $array[0], $species_id, $array[3], $array[4]);
}
}
if ($array[10]) { # Swissprot
if(defined($swissprot{$array[10]})){
$seen = 1;
$swissprot_count++;
XrefParser::BaseParser->add_to_xrefs($swissprot{$array[10]}, $array[0], '', $array[1], $array[2], "", $hgnc_swissprot_manual, $species_id);
$self->add_synonyms_for_hgnc($hgnc_swissprot_manual, $array[0], $species_id, $array[3], $array[4]);
}
}
}
if ($array[8]) { # RefSeq
if(defined($refseq{$array[8]})){
$seen = 1;
$refseq_count++;
XrefParser::BaseParser->add_to_xrefs($refseq{$array[8]}, $array[0], '', $array[1], $array[2], "", $hgnc_refseq_mapped, $species_id);
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_refseq_mapped, $arr, $species_id);
}
}
$self->add_synonyms_for_hgnc($hgnc_refseq_mapped, $array[0], $species_id, $array[3], $array[4]);
}
}
if(defined($array[5])){
if(defined($entrezgene{$array[5]})){
$seen = 1;
XrefParser::BaseParser->add_to_xrefs($entrezgene{$array[5]}, $array[0], '',
$array[1], $array[2], "", $hgnc_entrezgene_manual, $species_id);
$entrezgene_count++;
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_manual, $arr, $species_id);
}
}
$self->add_synonyms_for_hgnc($hgnc_entrezgene_manual, $array[0], $species_id, $array[3], $array[4]);
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_manual, $arr, $species_id);
}
}
}
}
}
if(defined($array[7])){
if(defined($entrezgene{$array[7]})){
$seen = 1;
XrefParser::BaseParser->add_to_xrefs($entrezgene{$array[7]}, $array[0], '',
$array[1], $array[2], "", $hgnc_entrezgene_mapped, $species_id);
$entrezgene_count++;
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_mapped, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_entrezgene_mapped, $arr, $species_id);
}
}
$self->add_synonyms_for_hgnc($hgnc_entrezgene_mapped, $array[0], $species_id, $array[3], $array[4]);
}
}
if(!$seen){ # Store to keep descriptions etc
$self->add_xref($array[0], "", $array[1], $array[2], $hgnc_desc_only, $species_id, "MISC");
if (defined($array[3])) { # dead name, add to synonym
my @array2 = split(',\s*', $array[3]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_desc_only, $arr, $species_id);
}
}
if (defined($array[4])) { # alias, add to synonym
my @array2 = split(',\s*', $array[4]);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($array[0], $hgnc_desc_only, $arr, $species_id);
}
}
$self->add_synonyms_for_hgnc($hgnc_desc_only, $array[0], $species_id, $array[3], $array[4]);
$mismatch++;
}
}
} # while HGNC
$hugo_io->close();
print "Loaded a total of " . ($refseq_count + $entrezgene_count + $swissprot_count) . " HGNC xrefs, $refseq_count from RefSeq curated mappings and $entrezgene_count from EntrezGene mappings $swissprot_count from Swissprot and $ensembl_count from ensembl_mapping\n" if($verbose);
print "$mismatch xrefs could not be associated via RefSeq, EntrezGene or ensembl\n" if($verbose);
return 0; # successful
}
sub add_synonyms_for_hgnc{
my $self = shift;
my $type = shift;
my $name = shift;
my $species_id = shift;
my $dead_name = shift;
my $alias = shift;
if (defined($dead_name)) { # dead name, add to synonym
my @array2 = split(',\s*', $dead_name);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($name, $type, $arr, $species_id);
}
}
if (defined($alias)) { # alias, add to synonym
my @array2 = split(',\s*', $alias);
foreach my $arr (@array2){
XrefParser::BaseParser->add_to_syn($name, $type, $arr, $species_id);
}
}
}
sub rename_url_file{
return "hugo.txt";
}
......
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