Initial data commit

Task/Bioinformatics-Sequence-mutation/Python/bioinformatics-sequence-mutation.py

@@ -0,0 +1,46 @@
+import random
+from collections import Counter
+
+def basecount(dna):
+    return sorted(Counter(dna).items())
+
+def seq_split(dna, n=50):
+    return [dna[i: i+n] for i in range(0, len(dna), n)]
+
+def seq_pp(dna, n=50):
+    for i, part in enumerate(seq_split(dna, n)):
+        print(f"{i*n:>5}: {part}")
+    print("\n  BASECOUNT:")
+    tot = 0
+    for base, count in basecount(dna):
+        print(f"    {base:>3}: {count}")
+        tot += count
+    base, count = 'TOT', tot
+    print(f"    {base:>3}= {count}")
+
+def seq_mutate(dna, count=1, kinds="IDSSSS", choice="ATCG" ):
+    mutation = []
+    k2txt = dict(I='Insert', D='Delete', S='Substitute')
+    for _ in range(count):
+        kind = random.choice(kinds)
+        index = random.randint(0, len(dna))
+        if kind == 'I':    # Insert
+            dna = dna[:index] + random.choice(choice) + dna[index:]
+        elif kind == 'D' and dna:  # Delete
+            dna = dna[:index] + dna[index+1:]
+        elif kind == 'S' and dna:  # Substitute
+            dna = dna[:index] + random.choice(choice) + dna[index+1:]
+        mutation.append((k2txt[kind], index))
+    return dna, mutation
+
+if __name__ == '__main__':
+    length = 250
+    print("SEQUENCE:")
+    sequence = ''.join(random.choices('ACGT', weights=(1, 0.8, .9, 1.1), k=length))
+    seq_pp(sequence)
+    print("\n\nMUTATIONS:")
+    mseq, m = seq_mutate(sequence, 10)
+    for kind, index in m:
+        print(f" {kind:>10} @{index}")
+    print()
+    seq_pp(mseq)