GOSlim parser

misc-scripts/xref_mapping/XrefParser/GOSlimParser.pm

+package XrefParser::GOSlimParser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+
+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 $user = "ensro";
+  my $host;
+  my $port = 3306;
+  my $dbname;
+  my $pass;
+  my $tran_name;
+
+
+  if($file =~ /host[=][>](\S+?)[,]/){
+    $host = $1;
+  }
+  if($file =~ /port[=][>](\S+?)[,]/){
+    $port =  $1;
+  }
+  if($file =~ /dbname[=][>](\S+?)[,]/){
+    $dbname = $1;
+  }
+  if($file =~ /pass[=][>](\S+?)[,]/){
+    $pass = $1;
+  }
+  if($file =~ /tran_name[=][>](\S+?)[,]/){
+    $tran_name = $1;
+  }
+
+  my $add_dependent_xref_sth = $self->dbi->prepare("INSERT INTO dependent_xref  (master_xref_id,dependent_xref_id, linkage_source_id) VALUES (?,?, $source_id)");
+
+  my $dbi2 = $self->dbi2($host, $port, $user, $dbname, $pass);
+
+  if(!defined($dbi2)){
+    return 1;
+  }
+
+  my (%go)   = %{XrefParser::BaseParser->get_valid_codes("GO",$species_id)};
+
+
+  my $count = 0;
+
+  my $xref_sth = $dbi2->prepare("SELECT t.accession, s.name, s.accession FROM term t, term s, aux_GO_goslim_goa_map ts WHERE ts.term_id = t.term_id and ts.subset_term_id = s.term_id");
+
+  $xref_sth->execute() or croak( $dbi2->errstr() );
+  while ( my @row = $xref_sth->fetchrow_array() ) {
+    my $term_acc     = $row[0];
+    my $desc         = $row[1];
+    my $subterm_acc  = $row[2];
+
+    if(defined($go{$term_acc})){
+      my $xref_id = $self->add_xref($subterm_acc, undef, $subterm_acc, $desc, $source_id, $species_id, "DEPENDENT");
+      $add_dependent_xref_sth->execute($go{$term_acc}, $xref_id);
+      $count++;
+    }
+
+  }
+  $xref_sth->finish;
+  print "Parsed GOSlim identifiers from $file, added $count dependent_xrefs\n" if($verbose);
+
+  return 0;
+}
+
+1;