Create Approximate Pattern Matching Problem

Author: Shivi91

Approximate Pattern Matching Problem

@@ -0,0 +1,45 @@
+#!/usr/bin/python3
+
+import sys
+
+def approximate_pattern_match_positions(pattern, sequence, d):
+        """
+        Approximate Pattern Matching Problem: Find all approximate occurrences of a pattern in a string.
+           Input: Two strings Pattern and Text along with an integer d.
+           Output: All positions where Pattern appears in Text with at most d mismatches.
+        """
+        
+        pattern_length = len(pattern)
+        pattern_positions = []
+        for i in range(len(sequence) - pattern_length + 1):
+                kmer = sequence[i:i+pattern_length]
+                if edit_distance(pattern, kmer) <= d:
+                        pattern_positions.append(str(i))
+                        
+        return pattern_positions
+
+
+def edit_distance(pattern1, pattern2):
+        """
+        Compare two patterns and calculate edit distance - the number of mismatches between the sequences
+        """
+        
+        edit_distance = 0
+        for i, nt in enumerate(pattern1):
+                if (nt != pattern2[i]):
+                        edit_distance += 1
+        
+        return edit_distance
+
+# Get filename from the command arguments and open the file
+filename = str(sys.argv[1])
+f = open(filename, 'r')
+
+# The first line in the file is the pattern
+pattern = f.readline().strip()
+sequence = f.readline().strip()
+allowed_mismatches = int(f.readline().strip())
+
+# Call function to calculate approximate pattern positions
+pattern_positions = approximate_pattern_match_positions(pattern, sequence, allowed_mismatches)
+print(' '.join(pattern_positions))