new parser to get ncRNA xrefs from the newly created xref ncRNA database

misc-scripts/xref_mapping/XrefParser/ncRNA_DBParser.pm

+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;