no longer used

misc-scripts/xref_mapping/XrefParser/Vega_TranParser.pm

-package XrefParser::Vega_TranParser;
-
-use strict;
-
-use DBI;
-
-use base qw( XrefParser::BaseParser );
-
-# Parse file of Vega transcript name records and assign direct xrefs
-# All assumed to be linked to transcripts
-
-sub run {
-
-  my ($self, $source_id, $species_id, $file) = @_;
-
-  die "No longer used try HGNC_curated_transcript\n";
-
-  my $vega_io = $self->get_filehandle($file);
-
-  my $clone_source_id =
-    $self->get_source_id_for_source_name('Clone_based_vega_transcript');
-  my $curated_source_id =
-    $self->get_source_id_for_source_name('HGNC_curated_transcript');
-  
-  if ( !defined $vega_io ) {
-    print STDERR "Could not open $file\n";
-    return 1;
-  }
-
-  my $xref_count = 0;
-  my $line_count = 0;
-  
-  my %vega_name;
-  my %vega_priority;
-
-  while ( $_ = $vega_io->getline() ) {
-    my $line_count++;
-    my ($stable_id, $name, $priority) = split;
-    
-    if(!defined($vega_name{$stable_id}) or $vega_priority{$stable_id} < $priority){
-      $vega_name{$stable_id} = $name;
-      $vega_priority{$stable_id} = $priority;
-    }	
-  }
-  
-
-  foreach my $stable_id (keys %vega_name){
-    my $name = $vega_name{$stable_id};
-    my $id = $curated_source_id;
-    if($name =~ /[.]/){
-      $id = $clone_source_id;
-    }
-    my $xref_id = $self->add_xref($name, "" , $name , "", $id, $species_id, "DIRECT");
-    $xref_count++;
-    
-    
-    $self->add_direct_xref($xref_id, $stable_id, "transcript", "");
-  }
-
-  print "Parsed $line_count lines from $file, added $xref_count xrefs and $xref_count direct_xrefs\n" if($verbose);
-
-  $vega_io->close();
-
-  return 0;
-}
-
-1;