pig is a merged species, needs some special methods to overwrite the default ones

misc-scripts/xref_mapping/XrefMapper/sus_scrofa.pm

+package XrefMapper::sus_scrofa;
+
+use  XrefMapper::BasicMapper;
+use  XrefMapper::SubmitMapper;
+use strict;
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::BasicMapper };
+
+
+sub gene_description_filter_regexps {
+
+  return ('^BA\S+\s+\(NOVEL PROTEIN\)\.?',
+	  '^DJ\S+\s+\(NOVEL PROTEIN\)\.?',
+	  '^LOC\d+\s*(PROTEIN)?\.?',
+	  '^Putative uncharacterized protein.*',
+	  '^ORF.*',
+	  '^PROTEIN C\d+ORF\d+\.*',
+	  '\(CLONE \S+\)\s+',
+	  '^BC\d+\_\d+\.?',
+	  '^CGI\-\d+ PROTEIN\.?\;?',
+	  '[0-9A-Z]{10}RIK PROTEIN[ \.]',
+	  'R\d{5}_\d[ \.,].*',
+	  'PROTEIN KIAA\d+[ \.].*',
+	  'RIKEN CDNA [0-9A-Z]{10}[ \.]',
+	  '^\(*HYPOTHETICAL\s+.*',
+	  '^UNKNOWN\s+.*',
+	  '^DKFZP[A-Z0-9]+\s+PROTEIN[\.;]?.*',
+	  '^CHROMOSOME\s+\d+\s+OPEN\s+READING\s+FRAME\s+\d+\.?.*',
+	  '^FKSG\d+\.?.*',
+	  '^HSPC\d+\s+PROTEIN\.?.*',
+	  '^KIAA\d+\s+PROTEIN\.?.*',
+	  '^KIAA\d+\s+GENE\s+PRODUCT\.?.*',
+	  '^HSPC\d+.*',
+	  '^PRO\d+\s+PROTEIN\.?.*',
+	  '^PRO\d+\.?.*',
+	  '^FLJ\d+\s+PROTEIN.*',
+	  '^PRED\d+\s+PROTEIN.*',
+	  '^WUGSC:.*\s+PROTEIN\.?.*',
+	  '^SIMILAR TO GENE.*',
+	  '^SIMILAR TO PUTATIVE[ \.]',
+	  '^SIMILAR TO HYPOTHETICAL.*',
+	  '^SIMILAR TO (KIAA|LOC).*',
+	  '^SIMILAR TO\s+$',
+          '^WUGSC:H_.*',
+          '^\s*\(?PROTEIN\)?\.?\s*$',
+	  '^\s*\(?FRAGMENT\)?\.?\s*$',
+          '^\s*\(?GENE\)?\.?\s*$',
+	  '^\s*\(\s*\)\s*$',
+          '^\s*\(\d*\)\s*[ \.]$');
+
+}
+
+
+sub get_official_name{
+   return "PIGGY";
+}
+
+sub get_canonical_name{
+   return "PIGGY";
+}
+
+# Not running transcript_names_from_gene for merged species
+# as this is already beng done in the OfficialNaming mapper
+sub transcript_names_from_gene {
+  return;
+}
+
+
+# For merged species, display xref assigned from the stable_table
+# which has been populated by the OfficialNaming mapper
+sub set_display_xrefs{
+  my $self = shift;
+  my $display = XrefMapper::DisplayXrefs->new($self);
+  $display->set_display_xrefs_from_stable_table();
+
+}
+
+
+
+
+1;