Raw content of XrefParser::ncRNA_DBParser
<![CDATA[package XrefParser::ncRNA_DBParser;
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: ncRNA_DBParser.pm file <source_id> <species_id> <verbose>\n\n";
exit(1);
}
run(@ARGV);
}
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 $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;
}
my %source;
$source{"RFAM"} = $self->get_source_id_for_source_name('RFAM') || die "Could not get source_id for RFAM";
$source{"miRBase"} = $self->get_source_id_for_source_name('miRBase') || die "Could not get source_id for miRBase";
my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
if(!defined($dbi2)){
return 1;
}
my $sql=(<<SQL);
SELECT transcript_stable_id, transcript_dbid, source, xref_name, xref_primary_id, xref_description
FROM ncRNA_Xref
WHERE taxonomy_id = $species_id
SQL
my ($stable_id, $dbid, $source_name, $label, $acc, $desc);
my $sth = $dbi2->prepare($sql);
$sth->execute() or croak( $dbi2->errstr() );
$sth->bind_columns(\$stable_id, \$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,"",$label,$description,$source{$source_name}, $species_id,"DIRECT");
$added++;
}
my $transcript_id = $dbid;
if(defined($stable_id) and $stable_id ne ""){
$transcript_id = $stable_id;
}
$self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));
}
$sth->finish;
print "Added $added Xrefs for ncRNAs\n" if($verbose);
return 0;
}
1;
]]>