Parses file of direct xrefs for Ig/TcR gene segments

misc-scripts/xref_mapping/XrefParser/SegmentParser.pm

+package XrefParser::SegmentParser;
+ 
+use strict;
+use POSIX qw(strftime);
+use File::Basename;
+ 
+use XrefParser::BaseParser;
+ 
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+# --------------------------------------------------------------------------------
+# Parse command line and run if being run directly
+
+if (!defined(caller())) {
+
+  if (scalar(@ARGV) != 1) {
+    print "\nUsage: SegmentParser.pm file <source_id> <species_id>\n\n";
+    exit(1);
+  }
+
+  run($ARGV[0]);
+
+}
+
+
+sub run {
+  my $self = shift if (defined(caller(1)));
+  my $file = shift;
+
+  my $source_id = shift;
+  my $species_id = shift;
+
+  if(!defined($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 %name_2_source_id=();
+  my $added=0;
+
+  if(!open(FILE,"<". $file)){
+    print  "ERROR: Could not open file $file\n";
+    return 1;
+  }
+  while(my $line = <FILE>){
+    chomp $line;
+    my ($gene_id,$transcript_id,$source_name,$acc,$display_label,$description, $status)
+      = split("\t",$line);
+
+    if(!defined($name_2_source_id{$source_name})){
+      my $tmp = $self->get_source_id_for_source_name($source_name);
+      if(!$tmp){
+	die("Could not get source_id for $source_name\n");
+      }
+      $name_2_source_id{$source_name} = $tmp;
+    }
+    my $xref_id = $self->get_xref($acc,$name_2_source_id{$source_name});
+    if(!defined($xref_id)){
+      $xref_id = $self->add_xref($acc,"",$display_label,$description,$name_2_source_id{$source_name}, $species_id);
+      $added++;
+    }
+    $self->add_direct_xref($xref_id, $transcript_id, "Transcript", "") if (defined($transcript_id));    
+
+    #just add to the transcript ONLY as the check at the end will move all
+    #the those mapped to the transcript to the genes anyway due to the
+    #biomart check
+  }
+  close FILE;
+
+  print "Added $added Xrefs for Gene segments\n";
+  return 0;
+}
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::SegmentParser";
+  return $self;
+
+}
+
+
+1;