From 12692e83055839a1187b7b1cf9fdfe4542738d8a Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 6 Feb 2020 18:04:10 +0100
Subject: [PATCH] Python export for HMM algorithm
---
modules/seq/alg/pymod/wrap_seq_alg.cc | 12 ++++++++++++
1 file changed, 12 insertions(+)
diff --git a/modules/seq/alg/pymod/wrap_seq_alg.cc b/modules/seq/alg/pymod/wrap_seq_alg.cc
index 9df107976..b2c116cdf 100644
--- a/modules/seq/alg/pymod/wrap_seq_alg.cc
+++ b/modules/seq/alg/pymod/wrap_seq_alg.cc
@@ -35,6 +35,8 @@
#include <ost/seq/alg/clip_alignment.hh>
#include <ost/seq/alg/distance_map.hh>
#include <ost/seq/alg/variance_map.hh>
+#include <ost/seq/alg/hmm_pseudo_counts.hh>
+#include <ost/seq/alg/hmm_score.hh>
using namespace boost::python;
using namespace ost::seq;
@@ -223,9 +225,19 @@ void export_distance_analysis()
;
}
+////////////////////////////////////////////////////////////////////
+// algorithms involving hmms
+void export_hmm_algorithms() {
+ def("AddAAPseudoCounts", &AddAAPseudoCounts, (arg("profile")));
+ def("AddTransitionPseudoCounts", &AddTransitionPseudoCounts, (arg("profile")));
+ def("HMMScore", &HMMScore, (arg("profile_0"), arg("profile_1"), arg("alignment"),
+ arg("s_0_idx"), arg("s_1_idx")));
+}
+
BOOST_PYTHON_MODULE(_ost_seq_alg)
{
export_aln_alg();
export_contact_prediction();
export_distance_analysis();
+ export_hmm_algorithms();
}
--
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