New Xref parser for Anopheles (AnoXcel data)

misc-scripts/xref_mapping/XrefParser/AnoXcelParser.pm

+package XrefParser::AnoXcelParser;
+
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+use base qw( XrefParser::BaseParser );
+
+# Parse the external description file
+#
+# Protein         mRNA            Location                Gene stable_id
+# AGAP004677-PB   AGAP004677-RB   2L:157496-159356:-1     AGAP004677
+# AGAP004677-PA   AGAP004677-RA   2L:157496-181213:-1     AGAP004677
+# AGAP004678-PA   AGAP004678-RA   2L:203866-204956:1      AGAP004678
+#...
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print STDERR "\nUsage: AnoXcelParser.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() ) {
+    chomp $line;
+    my ($protein_id, $mRNA_id, $loc, $gene_id) = split("\t",$line);  #and use the gene_id as accession
+
+    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, $gene_id, $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 $added Direct xrefs to genes for AnoXcel\n" if($verbose);
+  return 0;
+}
+1;
+