VectorBase PubMed parser

misc-scripts/xref_mapping/XrefParser/VBPubMedParser.pm

+package XrefParser::VBPubMedParser;
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+use base qw( XrefParser::BaseParser );
+
+# Parse the external description file
+#
+#PubMed ID      Stable ID       Feature Gene_ID (?)     Origin
+#1354853	AAEL009742	gene	AAEL009742	Inferred from UniProt entry ABDA_AEDAE (P29552)
+#1961751	AAEL006563	gene	AAEL006563	Inferred from UniProt entry VCP_AEDAE (P42660)
+#2052024	AAEL006424	gene	AAEL006424	Inferred from UniProt entry ALL2_AEDAE (P18153)
+
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print STDERR "\nUsage: VBPubMed.pm file <source_id> <species_id>\n\n";
+    exit(1);
+  }
+
+  run($ARGV[0]);
+
+}
+
+sub run {
+
+  my $self = shift if (defined(caller(1)));
+
+  my $source_id = shift;
+  my $species_id = shift;
+  my $files       = shift;
+  my $release_file   = shift;
+  my $verbose       = shift;
+
+  my $file = @{$files}[0];
+
+  print "source_id = $source_id, species= $species_id, file = $file\n" if($verbose);
+
+  if(!defined($source_id)){
+    $source_id = XrefParser::BaseParser->get_source_id_for_filename($file);
+  }
+  if(!defined($species_id)){
+    $species_id = XrefParser::BaseParser->get_species_id_for_filename($file);
+  }
+
+  my $added = 0;
+  my $count = 0;
+
+  my $file_io = $self->get_filehandle($file);
+
+  if ( !defined $file_io ) {
+    print STDERR "ERROR: Could not open file $file\n";
+    return 1;
+  }
+
+  while ( my $line = $file_io->getline() ) {
+    if ($line !~ /^#/) {
+
+      chomp $line;
+      my ($PubMed_id, $gene_id, $rien, $name, $origin) = split("\t",$line);  #and use the gene_id as accession
+      my $descr_full = "PubMed ID $PubMed_id - $origin\n" ;
+
+      print "PMID: $PubMed_id, GID: $gene_id, NONE: $rien, NOM: $name, ORI: $origin\n" ;
+
+      my $xref_id = $self->get_xref($gene_id,$source_id, $species_id);
+      if(!defined($xref_id)){
+	$xref_id = $self->add_xref($gene_id,"", $gene_id, $descr_full, $source_id, $species_id, "DIRECT");
+	$count++;
+      }
+      if(defined($gene_id) and $gene_id ne "-"){
+	$self->add_direct_xref($xref_id, $gene_id, "Gene", "") ;
+	$added++;
+      }	
+    }
+
+    $file_io->close();
+
+    print "Added $count xrefs and $added Direct xrefs to genes for VBPubMed\n" if($verbose);
+    return 0;
+  }
+}
+
+1;
+
+