new method pm used for RefSeq_mRNA,nc_RNA xrefs

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5.pm

+package XrefMapper::Methods::ExonerateGappedBest5;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+
+  return ('--gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '5');
+
+}
+
+sub query_identity_threshold {
+
+  return 90;
+
+}
+
+sub target_identity_threshold {
+
+  return 90;
+
+}
+
+
+1;

misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5_agam.pm

+package XrefMapper::Methods::ExonerateGappedBest5_agam;
+
+use XrefMapper::Methods::ExonerateBasic;
+
+use vars '@ISA';
+
+@ISA = qw{XrefMapper::Methods::ExonerateBasic};
+
+
+
+sub options {
+  return ('--gappedextension FALSE', '--model', 'affine:local', '--subopt', 'no', '--bestn', '5');
+}
+
+sub query_identity_threshold {
+  return 55;
+}
+
+sub target_identity_threshold {
+  return 55;
+}
+
+
+1;
+