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Commit 96ac2d90 authored by Monika Komorowska's avatar Monika Komorowska
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Parser replaced with VegaOfficialNameParser.pm

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misc-scripts/xref_mapping/XrefParser/HGNC_ENSTParser.pm deleted 100644 → 0
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package XrefParser::HGNC_ENSTParser;
use strict;
use DBI;
use Bio::EnsEMBL::Registry;
use base qw( XrefParser::BaseParser );
my $reg = "Bio::EnsEMBL::Registry";
# Parse file of HGNC records and assign direct xrefs
# All assumed to be linked to genes
sub run_script {
my $self = shift if (defined(caller(1)));
my $file = shift;
my $source_id = shift;
my $species_id = shift;
my $verbose = shift;
my ($type, $my_args) = split(/:/,$file);
my $host = "ens-staging1";
my $user = "ensro";
if($my_args =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
my $vuser;
my $vhost;
my $vport;
my $vdbname;
my $vpass;
if($my_args =~ /vhost[=][>](\S+?)[,]/){
$vhost = $1;
}
if($my_args =~ /vuser[=][>](\S+?)[,]/){
$vuser = $1;
}
if($my_args =~ /vport[=][>](\S+?)[,]/){
$vport = $1;
}
if($my_args =~ /vdbname[=][>](\S+?)[,]/){
$vdbname = $1;
}
else{
print "No vdbname??? $my_args??\n";
}
if($my_args =~ /vpass[=][>](\S+?)[,]/){
$vpass = $1;
}
my $cuser;
my $chost;
my $cport;
my $cdbname;
my $cpass;
if($my_args =~ /chost[=][>](\S+?)[,]/){
$chost = $1;
}
if($my_args =~ /cuser[=][>](\S+?)[,]/){
$cuser = $1;
}
if($my_args =~ /cport[=][>](\S+?)[,]/){
$cport = $1;
}
if($my_args =~ /cdbname[=][>](\S+?)[,]/){
$cdbname = $1;
}
if($my_args =~ /cpass[=][>](\S+?)[,]/){
$cpass = $1;
}
my $vega_dbc;
my $core_dbc;
if(defined($vdbname)){
print "Using $host $vdbname for Vega and $cdbname for Core\n";
$vega_dbc = $self->dbi2($vhost, $vport, $vuser, $vdbname, $vpass);
if(!defined($vega_dbc)){
print "Problem could not open connectipn to $vhost, $vport, $vuser, $vdbname, $vpass\n";
return 1;
}
$core_dbc = $self->dbi2($chost, $cport, $cuser, $cdbname, $cpass);
if(!defined($core_dbc)){
print "Problem could not open connectipn to $chost, $cport, $cuser, $cdbname, $cpass\n";
return 1;
}
}
else{
$reg->load_registry_from_db(
-host => $host,
-user => $user);
$vega_dbc = $reg->get_adaptor("human","vega","slice");
if(!defined($vega_dbc)){
print "Could not connect to human vega database using load_registry_from_db $host $user\n";
return 1;
}
$vega_dbc = $vega_dbc->dbc;
$core_dbc = $reg->get_adaptor("human","core","slice");
if(!defined($core_dbc)){
print "Could not connect to human core database using load_registry_from_db $host $user\n";
return 1;
}
$core_dbc= $core_dbc->dbc;
}
$source_id = XrefParser::BaseParser->get_source_id_for_source_name("HGNC","vega");
my $sql = 'select tsi.stable_id, x.display_label from xref x, object_xref ox , transcript_stable_id tsi, external_db e where e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and tsi.transcript_id = ox.ensembl_id and e.db_name like ?';
my $hgnc_sql = 'select tsi.stable_id, x.dbprimary_acc from xref x, object_xref ox , transcript_stable_id tsi, gene g, external_db e, transcript t where t.gene_id = g.gene_id and g.gene_id = ox.ensembl_id and tsi.transcript_id = t.transcript_id and e.external_db_id = x.external_db_id and x.xref_id = ox.xref_id and ox.ensembl_object_type = "Gene" and e.db_name like "HGNC"';
my %ott_to_hgnc;
my %ott_to_enst;
my $sth = $core_dbc->prepare($sql) || die "Could not prepare for core $sql\n";
foreach my $external_db (qw(OTTT shares_CDS_and_UTR_with_OTTT shares_CDS_with_OTTT Vega_transcript)){
$sth->execute($external_db) or croak( $core_dbc->errstr());
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[1]} = $row[0];
}
}
print "We have ".scalar(%ott_to_enst)." ott to enst entries\n " if($verbose);
$sth = $vega_dbc->prepare($hgnc_sql);
$sth->execute() or croak( $vega_dbc->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_hgnc{$row[0]} = $row[1];
}
$sth->finish;
print "We have ".scalar(%ott_to_hgnc)." ott to hgnc entries\n" if($verbose);
my $line_count = 0;
my $xref_count = 0;
# becouse the direct mapping have no descriptions etc
# we have to steal these fromt he previous HGNC parser.
# This is why the order states this is after the other one.
# maybe 1091,1092 is not right maybe should use name = HGNC and priority = 30r4 ??
my %label;
my %version;
my %description;
my $dbi = $self->dbi();
my $sql = "insert into synonym (xref_id, synonym) values (?, ?)";
my $add_syn_sth = $dbi->prepare($sql);
my $syn_hash = $self->get_hgnc_synonyms();
#get the source ids for HGNC refseq, entrezgene and unitprot
$sql = 'select source_id, priority_description from source where name like "HGNC"';
$sth = $dbi->prepare($sql);
$sth->execute();
my ($hgnc_source_id, $desc);
$sth->bind_columns(\$hgnc_source_id, \$desc);
my @arr;
while($sth->fetch()){
push @arr, $hgnc_source_id;
}
$sth->finish;
$sql = "select accession, label, version, description from xref where source_id in (".join(", ",@arr).")";
# print "$sql\n";;
$sth = $dbi->prepare($sql);
$sth->execute();
my ($acc, $lab, $ver);
my $hgnc_loaded_count = 0;
$sth->bind_columns(\$acc, \$lab, \$ver, \$desc);
while (my @row = $sth->fetchrow_array()) {
$label{$acc} = $lab;
$version{$acc} = $ver;
$description{$acc} = $desc;
$hgnc_loaded_count++;
}
$sth->finish;
if($hgnc_loaded_count == 0){
die "No point continuing no hgncs there\n";
}
my $ignore_count = 0;
my $ignore_examples ="";
my %acc;
foreach my $key ( keys %ott_to_hgnc){
if(defined($ott_to_enst{$key} )){
my $hgnc = $ott_to_hgnc{$key};
$hgnc =~ s/HGNC://;
my $stable_id = $ott_to_enst{$key};
if(!defined($label{$hgnc})){
$ignore_count++;
if($ignore_count < 10){
$ignore_examples .= " ".$hgnc;
}
next;
}
if(!defined($acc{$hgnc})){
my $version ="";
$line_count++;
my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
$acc{$hgnc} = $xref_id;
$xref_count++;
}
$self->add_direct_xref($acc{$hgnc}, $stable_id, "transcript", "");
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($acc{$hgnc}, $syn);
}
}
}
}
$add_syn_sth->finish;
print "Parsed $line_count HGNC identifiers from $file, added $xref_count xrefs and $line_count direct_xrefs\n" if($verbose);
if($ignore_count){
print $ignore_count." ignoreed due to numbers no identifiers being no longer valid :- $ignore_examples\n" if($verbose);
}
return 0;
}
1;
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