Proto-parser for CCDS identifiers.

misc-scripts/xref_mapping/XrefParser/CCDSParser.pm

+package XrefParser::CCDSParser;
+
+use strict;
+use File::Basename;
+
+use XrefParser::BaseParser;
+
+use vars qw(@ISA);
+@ISA = qw(XrefParser::BaseParser);
+
+# Parse file of CCDS records and assign direct xrefs
+# All assumed to be linked to transcripts
+
+sub run {
+
+  my ($self, $file, $source_id, $species_id) = @_;
+
+  open(CCDS,"<".$file) || die "Could not open $file\n";
+
+  my $count = 0;
+
+  while (<CCDS>) {
+
+    # TODO extract stable ID, CCDS identifier
+    my ($stable_id, $ccds) = split;
+
+    my $xref_id = $self->add_xref($ccds, 1, $ccds, "", $source_id, $species_id);
+    $self->add_direct_xref($xref_id, $stable_id, "transcript", "");
+    $count++;
+
+  }
+
+  print "Parsed $count CCDS identifiers from $file\n";
+
+}
+
+
+sub new {
+
+  my $self = {};
+  bless $self, "XrefParser::CCDSParser";
+  return $self;
+
+}
+
+1;