blastn style alignment option

sodiumnitrate · Oct 11, 2023 · 4e72b77 · 4e72b77
1 parent 09e6d09
commit 4e72b77
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Showing 5 changed files with 34 additions and 3 deletions.
diff --git a/src/include/pair_score.hpp b/src/include/pair_score.hpp
@@ -16,5 +16,6 @@ class PairScore{
 
     void init_blosum50();
     void init_blosum62();
+    void init_blastn();
     int query(char res1, char res2);
 };
diff --git a/src/include/pairwise_aligner.hpp b/src/include/pairwise_aligner.hpp
@@ -23,6 +23,7 @@ class PairwiseAligner{
     PairScore* ps;
 public:
     PairwiseAligner();
+    PairwiseAligner(std::string scoring);
     void set_algorithm(std::string alg);
     std::string get_algorithm();
     void set_query(std::string query_);

diff --git a/src/pair_score.cpp b/src/pair_score.cpp
@@ -6,9 +6,29 @@ PairScore::PairScore(std::string name_)
     std::cout << name << std::endl;
     if (name.compare("blosum50") == 0) init_blosum50();
     else if (name.compare("blosum62") == 0) init_blosum62();
+    else if (name.compare("blastn") == 0) init_blastn();
     else throw "unrecognized name";
 }
 
+void PairScore::init_blastn(){
+    scores.clear();
+    std::string letters = "ACGTU";
+
+    for(auto let1 : letters){
+        for (auto let2 : letters){
+            std::string pair;
+            pair.push_back(let1);
+            pair.push_back(let2);
+            if (let1 == let2){
+                scores[pair] = 1;
+            }
+            else{
+                scores[pair] = -2;
+            }
+        }
+    }
+}
+
 void PairScore::init_blosum50(){
     scores.clear();
     // load data and populate map

diff --git a/src/pairwise_aligner.cpp b/src/pairwise_aligner.cpp
@@ -14,11 +14,13 @@
 
 namespace py = pybind11;
 
-enum algorithms {local, global};
-
 PairwiseAligner::PairwiseAligner(){
     ps = new PairScore("blosum50");
 };
+PairwiseAligner::PairwiseAligner(std::string scoring){
+    set_gap_penalty(-2);
+    ps = new PairScore(scoring);
+}
 void PairwiseAligner::set_algorithm(std::string alg) {algorithm = alg;}
 std::string PairwiseAligner::get_algorithm() {return algorithm;}
 void PairwiseAligner::set_query(std::string query_) {query = query_;}

diff --git a/tests/test_pairwise_aligner.py b/tests/test_pairwise_aligner.py
@@ -38,4 +38,11 @@ def test_align_2(self):
 
         pa.align()
 
-        pdb.set_trace()
+    def test_align_blastn(self):
+        pa = PairwiseAligner("blastn")
+        pa.algorithm = "local"
+
+        pa.target = "GGTACGTACG"
+        pa.query = "ACCT"
+
+        pa.align()