--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/igm_naive_mutations.py	Mon Dec 12 12:32:44 2022 +0000
@@ -0,0 +1,46 @@
+#!/usr/bin/env python3
+
+"""
+Find naive mutations (< 2% mutated) for IGM genes
+"""
+
+import argparse
+import contextlib
+
+
+def find_naive_mutations(mutation_file, naive_file, naive_memory_file,
+                         percentage_cutoff=0.02):
+    # A compound with statement throws a syntax error with the included python
+    # 3.7.1 in the container, so use an exit stack instead.
+    with contextlib.ExitStack() as stack:
+        mutations = stack.enter_context(open(mutation_file, "rt"))
+        naive = stack.enter_context(open(naive_file, "wt"))
+        naive_memory = stack.enter_context(open(naive_memory_file, "wt"))
+        header = next(mutations)
+        naive.write(header)
+        naive_memory.write(header)
+        for line in mutations:
+            sequence_id, best_match, mutation_no, region_length, _ = \
+                line.strip('\n').split('\t')
+            if best_match != "IGM":
+                continue
+            mutation_no = int(mutation_no)
+            region_length = int(region_length)
+            if (mutation_no / region_length) < percentage_cutoff:
+                naive.write(line)
+            else:
+                naive_memory.write(line)
+
+
+def main():
+    parser = argparse.ArgumentParser()
+    parser.add_argument("mutation_file", help="scatter.txt")
+    parser.add_argument("naive_file")
+    parser.add_argument("naive_memory_file")
+    args = parser.parse_args()
+    find_naive_mutations(args.mutation_file, args.naive_file,
+                         args.naive_memory_file)
+
+
+if __name__ == "__main__":
+    main()
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