XrefParser::EG_DBParser Class Reference
Public Member Functions | |
| public | run_script () |
Detailed Description
Definition at line 5 of file EG_DBParser.pm.
Member Function Documentation
◆ run_script()
| public XrefParser::EG_DBParser::run_script | ( | ) |
Undocumented method
Code:
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sub run_script {
my ($self, $ref_arg) = @_;
my $source_id = $ref_arg->{source_id};
my $species_id = $ref_arg->{species_id};
my $file = $ref_arg->{file};
my $verbose = $ref_arg->{verbose};
if((!defined $source_id) or (!defined $species_id) or (!defined $file) ){
croak "Need to pass source_id, species_id and file as pairs";
}
$verbose |=0;
print STDERR "parsing EG_DB_Xrefs...\n";
my ($type, $my_args) = split(/:/,$file);
my $user ="ensro";
my $host;
my $port;
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 = $1;
}
if($my_args =~ /user[=][>](\S+?)[,]/){
$user = $1;
}
print STDERR "species_id, $species_id\n";
my %source;
# Todo: get the whole list of sources for All EG set
my $sources_aref = ['Mycgr3_jgi_v2.0_gene', 'BROAD_U_maydis','CADRE','CADRE_Afum_A1163','AspGD','ENA_GENE','BROAD_F_oxysporum','BROAD_G_moniliformis','BROAD_G_zeae','GeneDB','BROAD_P_infestans','phyra_jgi_v1.1','physo1_jgi_v1.1','PGD_GENE','phatr_jgi_v2_bd','phatr_jgi_v2','thaps_jgi_v2','thaps_jgi_v2_bd','SCHISTODB','triad_jgi_v1.0'];
foreach my $source_name (@$sources_aref) {
$source{$source_name} = $self->get_source_id_for_source_name($source_name) || die "Could not get source_id for $source_name\n";
}
my $db = XrefParser::Database->new({ host => $host,
port => $port,
user => $user,
dbname => $dbname,
pass => $pass});
my $dbi2 = $db->dbi();
if(!defined($dbi2)){
print STDERR "failed to connect to EG_Xrefs database!\n";
return 1;
}
my $sql=(<<"SQL");
SELECT gene_stable_id, transcript_stable_id, gene_dbid, transcript_dbid,
source, xref_name, xref_primary_id, xref_description
FROM EG_Xref
WHERE taxonomy_id = $species_id
SQL
my ($gene_stable_id, $transcript_stable_id, $gene_dbid, $transcript_dbid, $source_name, $label, $acc, $desc);
my $sth = $dbi2->prepare($sql);
$sth->execute() or croak( $dbi2->errstr() );
$sth->bind_columns(\$gene_stable_id, \$transcript_stable_id, \$gene_dbid, \$transcript_dbid, \$source_name, \$label, \$acc, \$desc);
my $added = 0;
while ( $sth->fetch() ) {
my ($description,$junk) = split("[[]Source:",$desc);
if(!defined($source{$source_name})){
print STDERR "Could not find source_id for source $source_name for xref $acc\n";
next;
}
my $xref_id = $self->get_xref($acc,$source{$source_name}, $species_id);
if(!defined($xref_id)){
$xref_id = $self->add_xref({ acc => $acc,
label => $label,
desc => $description,
source_id => $source{$source_name},
species_id => $species_id,
info_type => "DIRECT"} );
$added++;
}
my $transcript_id = $transcript_dbid;
if(defined($transcript_stable_id) and $transcript_stable_id ne ""){
$transcript_id = $transcript_stable_id;
}
my $gene_id = $gene_dbid;
if(defined($gene_stable_id) and $gene_stable_id ne ""){
$gene_id = $gene_stable_id;
}
#$self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));
$self->add_direct_xref($xref_id, $gene_id, "Gene", "") if (defined($gene_id));
}
$sth->finish;
print "Added $added Xrefs for EGs\n" if($verbose);
return 0;
}
The documentation for this class was generated from the following file:
- ensembl/misc-scripts/xref_mapping/XrefParser/EG_DBParser.pm
