Script to convert new xref mappings (which may be to translations or...

Script to convert new xref mappings (which may be to translations or transcripts) to all translations

misc-scripts/xref_mapping/convert_xrefs_to_all_translations.pl

+# New xref system maps xrefs to ensembl translations, transcripts etc
+# Old mappings are always to translations, so need to convert new mappings
+# to be all translations in order to facilitate comparison.
+
+use strict;
+use Getopt::Long;
+use Bio::EnsEMBL::DBSQL::DBAdaptor;
+
+my $host   = 'ecs2';
+my $port   = 3365;
+my $user   = 'ensro';
+my $dbname = 'homo_sapiens_core_26_35';
+my $file;
+
+GetOptions ('file=s'  => \$file);
+
+die "Must specify -file argument" if (!$file);
+
+my $db = new Bio::EnsEMBL::DBSQL::DBAdaptor(-host   => $host,
+                                            -user   => $user,
+					    -port   => $port,
+                                            -dbname => $dbname);
+
+my $transcript_adaptor = $db->get_TranscriptAdaptor();
+my $translation_adaptor = $db->get_TranslationAdaptor();
+
+# loop over each mapping in the file and convert if necessary
+
+open(FILE, $file) || die "Could not open $file\n";
+
+#print <FILE>; # echo header
+
+while (<FILE>) {
+
+  my ($xref_id, $type, $ensembl_id) = split;
+
+  # Just echo Translation mappings unchanged
+  print if ($type =~ /Translation/i);
+
+  # Convert transcripts to translations
+  if ($type =~ /Transcript/i) {
+    my $translation_id = get_translation_for_transcript($ensembl_id);
+    print "$xref_id\tTranslation\t$translation_id\n" if ($translation_id);
+  }
+
+  # Other types here ...
+}
+
+close(FILE);
+
+# ----------------------------------------------------------------------
+
+sub get_translation_for_transcript {
+
+  my $transcript_id = shift;
+
+  my $transcript = $transcript_adaptor->fetch_by_dbID($transcript_id);
+  my $translation = $translation_adaptor->fetch_by_Transcript($transcript);
+
+  return undef if (!$translation);
+
+  return $translation->dbID();
+
+}
+