Raw content of XrefParser::MGI_Vega_Parser
<![CDATA[package XrefParser::MGI_Vega_Parser;
use strict;
use File::Basename;
use base qw( XrefParser::BaseParser );
use strict;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
#my $dbi2;
if (!defined(caller())) {
if (scalar(@ARGV) != 1) {
print STDERR "\nUsage: MGI_Vega_Parser.pm file <source_id> <species_id>\n\n";
exit(1);
}
run(@ARGV);
}
sub run_script {
my ($self, $file, $source_id, $species_id, $verbose) = @_;
my ($type, $my_args) = split(/:/,$file);
my $user = "ensro";
my $host ="ens-staging";
my $port = "3306";
my $dbname = "";
my $pass;
if($my_args =~ /host[=][>](\S+?)[,]/){
$host = $1;
}
if($my_args =~ /port[=][>](\S+?)[,]/){
$port = $1;
}
if($my_args =~ /dbname[=][>](\S+?)[,]/){
$dbname = $1;
}
if($my_args =~ /pass[=][>](\S+?)[,]/){
$pass = $1;
}
$source_id = XrefParser::BaseParser->get_source_id_for_source_name("MGI","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 "MGI"';
my %ott_to_hgnc;
my %ott_to_enst;
my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
if(!defined($dbi2)){
return 1;
}
my $sth = $dbi2->prepare($sql); # funny number instead of stable id ?????
$sth->execute("ENST_CDS") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
$sth = $dbi2->prepare($sql);
$sth->execute("ENST_ident") or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_enst{$row[0]} = $row[1];
}
$sth->finish;
print "We have ".scalar(%ott_to_enst)." ott to enst entries\n " if($verbose);
$sth = $dbi2->prepare($hgnc_sql);
$sth->execute() or croak( $dbi2->errstr() );
while ( my @row = $sth->fetchrow_array() ) {
$ott_to_hgnc{$row[0]} = $row[1];
}
$sth->finish;
print "We have ".scalar(%ott_to_hgnc)." ott to mgi entries\n" if($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 "MGI"';
$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})){
$acc{$hgnc} = 1;
my $version ="";
$line_count++;
my $xref_id = $self->add_xref($hgnc, $version{$hgnc} , $label{$hgnc}||$hgnc , $description{$hgnc}, $source_id, $species_id, "DIRECT");
$xref_count++;
$self->add_direct_xref($xref_id, $stable_id, "transcript", "");
if(defined($syn_hash->{$hgnc})){
foreach my $syn (@{$syn_hash->{$hgnc}}){
$add_syn_sth->execute($xref_id, $syn);
}
}
}
}
}
$add_syn_sth->finish;
print "Parsed $line_count MGI 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;
]]>