From ad7aab1caabedfaacccfac80a16e03959839f230 Mon Sep 17 00:00:00 2001
From: Monika Komorowska <mk8@sanger.ac.uk>
Date: Mon, 9 Jan 2012 14:50:57 +0000
Subject: [PATCH] new method pm used for RefSeq_mRNA,nc_RNA xrefs
---
.../Methods/ExonerateGappedBest5.pm | 30 +++++++++++++++++++
.../Methods/ExonerateGappedBest5_agam.pm | 25 ++++++++++++++++
2 files changed, 55 insertions(+)
create mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5.pm
create mode 100644 misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5_agam.pm
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5.pm
new file mode 100644
index 0000000000..abbe448361
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5.pm
@@ -0,0 +1,30 @@
+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;
diff --git a/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5_agam.pm b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5_agam.pm
new file mode 100644
index 0000000000..9dd437be86
--- /dev/null
+++ b/misc-scripts/xref_mapping/XrefMapper/Methods/ExonerateGappedBest5_agam.pm
@@ -0,0 +1,25 @@
+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;
+
--
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