Parser to add direct mapping fro swissprot entrys

misc-scripts/xref_mapping/XrefParser/UniProtDirectParser.pm

+package XrefParser::UniProtDirectParser;
+
+use strict;
+
+use DBI;
+
+use base qw( XrefParser::BaseParser );
+
+# Parse file of Uniprot records and assign direct xrefs
+# All assumed to be linked to translation
+
+my $verbose;
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print "\nUsage: RefSeqParser.pm file.SPC <source_id> <species_id>\n\n";
+    exit(1);
+  }
+
+  run($ARGV[0], -1);
+
+}
+
+# --------------------------------------------------------------------------------
+
+sub run {
+
+  my $self = shift if (defined(caller(1)));
+
+  my $source_id  = shift;
+  my $species_id = shift;
+  my $files  = shift;
+  my $rel_file   = shift;
+  $verbose       = shift;
+
+  my %prefix = (9606 => "ENSP0", 10090 => "ENSMUSP0", 10116 => "ENSRNOP0");
+
+  if(!defined($prefix{$species_id})){
+    print "No prefix known for this species $species_id???\n";
+    return 1;
+  }
+
+  my $filename = @{$files}[0];
+
+  my $file_io = $self->get_filehandle($filename);
+  if ( !defined($file_io) ) {
+    return 1;
+  }
+
+  my $parsed_count = 0;
+
+
+  my %prot2ensembl;
+
+  my $count = 0;
+  while ( defined( my $line = $file_io->getline() ) ) {
+    my ($prot, $ens) = split /\s+/,$line;
+    if($ens =~ /$prefix{$species_id}/){
+      push @{$prot2ensembl{$prot}}, $ens;
+   }
+  }
+  my $dbi = XrefParser::BaseParser->dbi();
+
+  my $sw_source_id =  XrefParser::BaseParser->get_source_id_for_source_name("uniprot/swissprot","sequence_mapped");
+  if($sw_source_id < 1){
+    die "Could not find source id for uniprot/swissprot ???\n";
+  }
+  else{
+    print "Source_id = $sw_source_id\n";
+  }
+  my $get_desc_sth = $dbi->prepare("select xref_id, version, label, description from xref where source_id = $sw_source_id and accession = ?");
+
+
+  my $get_dependents_sth = $dbi->prepare("select dependent_xref_id, linkage_annotation, linkage_source_id  from dependent_xref where master_xref_id = ?");
+
+  my $add_dependent_xref_sth = $dbi->prepare("INSERT INTO dependent_xref (master_xref_id,dependent_xref_id,linkage_annotation, linkage_source_id) VALUES (?,?,?,?)");
+
+  my $err_count;
+  foreach my $key (keys %prot2ensembl){
+
+    #
+    # get the descrptions etc for the uniprot entry
+    #
+    $get_desc_sth->execute($key);
+    my ($old_xref_id, $version, $label, $description);
+    $get_desc_sth->bind_columns(\$old_xref_id, \$version, \$label, \$description);
+    $get_desc_sth->fetch;
+    if(!defined($old_xref_id)){
+      print STDERR "Could not find $key in the database\n" if ($err_count <10);
+      $err_count++;
+      next;
+    }
+    $count++;
+
+    #
+    # get the dependents
+    #
+    my %linkage_anotation=();
+    my %linkage_source_id=();
+    my ($dependent_xref_id, $linkage_annotation, $linkage_source_id);
+    $get_dependents_sth->execute($old_xref_id);
+    $get_dependents_sth->bind_columns(\$dependent_xref_id, \$linkage_annotation, \$linkage_source_id);
+    while($get_dependents_sth->fetch){
+      $linkage_anotation{$dependent_xref_id} =  $linkage_annotation;
+      $linkage_source_id{$dependent_xref_id} =  $linkage_source_id;
+    }
+
+
+#    print $key."\t";
+    #
+    # Add the new xref
+    #
+
+    my $xref_id = XrefParser::BaseParser->add_xref($key, $version, $label, $description, $source_id, $species_id, "DIRECT");
+    foreach my $trans (@{$prot2ensembl{$key}}){
+      #
+      #add the direct xref entry
+      #
+
+      XrefParser::BaseParser->add_direct_xref( $xref_id, $trans, "Translation", '');
+#      print ":".$trans;
+
+      #
+      #add the dependents
+      #
+      foreach my $dep (keys %linkage_anotation){
+	$add_dependent_xref_sth->execute($xref_id, $dep, $linkage_anotation{$dep}, $linkage_source_id{$dep});	
+      }
+    }
+  }
+
+
+  print $count." entrys added\n".$err_count." not found\n";
+  return 0;
+}
+
+
+1;