added functionality to query the range of alignment for target and qu…

…ery separately

src/sequence_analysis/pairwise_aligner.py

@@ -37,3 +37,25 @@ def print(self, char_per_line=80):
             print(query_aligned[i*char_per_line:(i+1)*char_per_line])
             print(match[i*char_per_line:(i+1)*char_per_line])
             print(target_aligned[i*char_per_line:(i+1)*char_per_line])
+
+
+    # TODO: refactor below.
+    def get_query_range(self):
+        """
+        Function to get the range of the query that aligns with the target.
+        """
+        query_aligned = self.get_query_aligned().replace('-','')
+        start = self.query.find(query_aligned)
+        end = self.query[::-1].find(query_aligned[::-1])
+        end = len(self.query) - end - 1
+        return start, end
+
+    def get_target_range(self):
+        """
+        Function to get the range of the target that aligns with the query.
+        """
+        target_aligned = self.get_target_aligned().replace('-','')
+        start= self.target.find(target_aligned)
+        end = self.target[::-1].find(target_aligned[::-1])
+        end = len(self.target) - end - 1
+        return start, end

tests/test_pairwise_aligner.py

@@ -48,6 +48,21 @@ def test_align_3(self):
         pa.target = "MKA"
         pa.align()
 
+    def test_get_alignment_range(self):
+        pa = PairwiseAligner()
+        pa.algorithm = "local"
+        pa.query = "MCDDVAALVVD"
+        pa.target = "DVAALV"
+        pa.align()
+
+        qs, qe = pa.get_query_range()
+        assert qs == 3
+        assert qe == 8
+
+        ts, te = pa.get_target_range()
+        assert ts == 0
+        assert te == len(pa.target)-1
+
     def test_align_blastn(self):
         pa = PairwiseAligner("blastn", -2)
         pa.algorithm = "local"