find pattern

pattern_finding/find_pattern.py

@@ -0,0 +1,61 @@
+#!/usr/bin/env python3
+"""
+Author : loicborcard <loicborcard@localhost>
+Date   : 2022-11-19
+Purpose: find pattern in a DNA sequence
+"""
+
+import argparse
+
+
+# --------------------------------------------------
+def get_args():
+    """Get command-line arguments"""
+
+    parser = argparse.ArgumentParser(
+        description='Rock the Casbah',
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter)
+
+
+    parser.add_argument('-f',
+                        '--file',
+                        help='A readable file',
+                        metavar='FILE',
+                        type=argparse.FileType('rt'),
+                        default=None)
+
+
+    return parser.parse_args()
+
+
+# --------------------------------------------------
+def main():
+    """find the number of occurences in a dna string"""
+
+    args = get_args()
+    file_arg = args.file
+
+    dna_str = file_arg.readline().rstrip('\n')
+    pat = file_arg.readline().rstrip('\n') # rstrip('\n') remove the newline at each line
+    print(dna_str,pat)
+
+    # lengths of the motif and the dna string
+    k = len(pat)
+    s = len(dna_str)
+    # store the position of the pattern
+    pos = []
+
+    for i in range(0,s):
+        cur_str = dna_str[i:k+i]
+        if cur_str == pat:
+            # take the position where the motif is found
+            pos.append(str(i+1))
+
+    print(" ".join(pos))
+
+
+
+
+# --------------------------------------------------
+if __name__ == '__main__':
+    main()

pattern_finding/test.txt

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+GATATATGCATATACTT
+ATAT