PHIbase parser

misc-scripts/xref_mapping/XrefParser/PHIbaseParser.pm

+package XrefParser::PHIbaseParser;
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+
+use XML::LibXML;
+
+use base qw( XrefParser::BaseParser );
+
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print "\nUsage: PhibaseParser.pm file <source_id> <species_id>\n\n";
+    exit(1);
+  }
+
+  print STDERR "ARGV[0]: $ARGV[0]\n";
+
+  run($ARGV[0]);
+
+}
+
+sub run {
+
+  my $self = shift if (defined(caller(1)));
+
+  my $source_id    = shift;
+  my $species_id   = shift;
+  #my $phi_xml_file = shift;
+  my $files        = shift;
+  my $verbose      = shift;
+
+  my $phi_xml_file = @{$files}[0];
+  
+  print STDERR "PhiBase file to parse, $phi_xml_file\n";
+
+  my %phi_mapping;
+  my %taxIds;
+
+  my $term = undef;
+  my $desc = undef;
+  
+  my $phi_parser = XML::LibXML->new();
+  my $phi_doc    = $phi_parser->parse_file($phi_xml_file);
+
+  my $concepts_count = 0;
+  
+  foreach my $concept ($phi_doc->findnodes('ondex:ondexdata/ondexdataseq/concepts/concept')) {
+
+      #print STDERR "parsing concept...\n";
+
+      my ($pid_node) = $concept->findnodes('./pid');
+      my $pid = $pid_node->to_literal;
+
+      #print STDERR "pid, $pid\n";
+
+    my $concept_accessions_aref = $concept->findnodes('./coaccessions/concept_accession');
+    my $uniprot_acc = undef;
+    foreach my $concept_accession (@$concept_accessions_aref) {
+	
+	# get the one associated with UniProt
+
+	my ($elementOf) = $concept_accession->findnodes('./elementOf');
+
+	# print STDERR "elementOf: " . $elementOf->to_literal . "\n";
+
+	if ($elementOf->to_literal =~ /UPROT/) {
+	    my ($accession) = $concept_accession->findnodes('./accession');
+	    $uniprot_acc = $accession->to_literal;
+
+	    #print STDERR "UniProt: $uniprot_acc\n";
+	    
+	}
+    }
+
+    if (!defined $uniprot_acc) {
+	print STDERR "phi id, $pid, no uniprot mapping found in xml file!\n";
+    }
+    else {
+	if (!defined $phi_mapping{$uniprot_acc}) {
+	    $phi_mapping{$uniprot_acc} = 
+		{
+		    -phi_ids => [$pid],
+		    -tax_id  => undef,
+		};
+	}
+	else {
+	    my $phi_href = $phi_mapping{$uniprot_acc};
+	    my $aref = $phi_href->{-phi_ids};
+	    push (@$aref, $pid);
+	}
+    }
+
+      # Get the TaxId
+
+      my $concept_gds_aref = $concept->findnodes('./cogds/concept_gds');
+      my $taxId = undef;
+      
+      foreach my $concept_gds (@$concept_gds_aref) {
+	  
+	  # get the one associated with Taxid
+	  
+	  my ($attrname) = $concept_gds->findnodes('./attrname');
+	  
+	  if ($attrname->to_literal =~ /TAXID/) {
+	      my ($value) = $concept_gds->findnodes('./value');
+	      $taxId = $value->to_literal;
+	      $taxId =~ s/\D//g;
+	      
+	      #print STDERR "taxId: $taxId\n";
+
+	      if (! defined $taxIds{$taxId}) {
+		  $taxIds{$taxId} = 1;
+	      }
+
+	      if (defined $uniprot_acc) {
+		  my $phi_href = $phi_mapping{$uniprot_acc};
+		  $phi_href->{-tax_id} = $taxId;
+	      }
+	  }
+      }
+      
+      #print STDERR "parsing concept done\n\n";
+      
+      $concepts_count++;
+  }
+  
+  my @phis = keys (%phi_mapping);
+
+  print STDERR "Parsed $concepts_count concepts\n";
+  print STDERR "Found " . @phis . " with UniProt mapping!\n";
+
+  print STDERR "Found " . keys (%taxIds) . " different taxIds\n";
+  
+  #get the "main" PHIbase source id.
+  $source_id = $self->get_source_id_for_source_name("PHIbase");
+
+
+  #get the mapping that are already there so that we don't get lots of duplicates.
+  # stored in the global hash xref_dependent_mapped.
+  $self->get_dependent_mappings($source_id);
+
+  #if(!defined($species_id)){
+  #  $species_id = $self->get_species_id_for_filename($phi_xml_file);
+  #}
+
+  my $swiss_miss=0;
+  my (%swiss) = %{$self->get_valid_codes("uniprot/", $species_id)};
+
+  print STDERR "got " . keys (%swiss) . " Uniprot entries\n";
+   
+  print STDERR "species_id, source_id: $species_id, $source_id\n";
+
+  foreach my $uniprot_acc (keys (%phi_mapping)) {
+      my $phis_href = $phi_mapping{$uniprot_acc};
+      my $taxId = $phis_href->{-tax_id};
+      if ($taxId eq $species_id) {
+
+	  print STDERR "Adding xrefs for UniProt, $uniprot_acc\n";
+
+	  # Get the master_xref_id
+	  # and the linkage
+	  
+	  my $master_xref_id = $swiss{$uniprot_acc};
+
+	  if (!defined $master_xref_id) {
+	      print STDERR "failed to get the master_xref_if for UniProt, $uniprot_acc!\n";
+	      # one reason it happens is that the UniProt identifier is attached to a different tax node in Phibase that it is in UniProt
+	  }
+	  else {
+	      print STDERR "master_xref_id, $master_xref_id\n";
+	      
+	      my $linkage = undef;
+	      
+	      my $phis_aref = $phis_href->{-phi_ids};
+	      foreach my $phibase_id (@$phis_aref) {
+		  print STDERR "Adding xrefs for phibase id, $phibase_id\n";
+		  $self->add_to_xrefs($master_xref_id,$phibase_id,'',$phibase_id,'',$linkage,$source_id,$species_id);
+	      }
+	  }
+
+      }
+  }
+
+  return 0;
+
+}
+
+1;