For running Culex Xrefs

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest1_culex.pm

+package XrefMapper::Methods::ExonerateGappedBest1_culex;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+
+  return ('--gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '1');
+
+}
+
+sub query_identity_threshold {
+  return 55;
+}
+
+sub target_identity_threshold {
+  return 55;
+}
+
+
+1;

misc-scripts/xref_mapping/XrefMapper/culex_pipiens.pm

+
+package XrefMapper::culex_pipiens;
+
+use  XrefMapper::BasicMapper;
+use  XrefMapper::VBCoordinateMapper;
+
+use vars '@ISA';
+
+@ISA = qw{ XrefMapper::BasicMapper };
+
+sub get_set_lists {
+
+  return [["ExonerateGappedBest1_culex", ["culex_pipiens","*"]]];
+
+}
+
+# transcript, gene display_xrefs can use defaults
+# since anopheles_symbol is "before" Uniprot
+
+# If there is an Anopheles_symbol xref, use its description
+sub gene_description_sources {
+
+  return ("Anopheles_symbol",
+	  "Uniprot/SWISSPROT",
+	  "RefSeq_peptide",
+	  "RefSeq_dna",
+	  "Uniprot/SPTREMBL",
+	  #"RefSeq_peptide_predicted",
+	  #"RefSeq_dna_predicted",
+	  #"EntrezGene");
+          );
+}
+
+sub transcript_display_xref_sources {
+
+  my @list = qw(RFAM
+		miRBase
+		Uniprot/SWISSPROT
+		Uniprot/Varsplic
+		Uniprot/SPTREMBL);
+
+  my %ignore;
+  return [\@list,\%ignore];
+
+}
+
+# regexps to match any descriptons we want to filter out
+sub gene_description_filter_regexps {
+
+  return ();
+
+}
+
+1;