--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/bin/qual_confirm.py	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,107 @@
+#!/usr/bin/env python3
+
+# Kranti Konganti
+
+import argparse
+import inspect
+import logging
+import os
+import pprint
+
+
+# Multiple inheritence for pretty printing of help text.
+class MultiArgFormatClasses(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
+    pass
+
+
+# Main
+def main() -> None:
+    """
+    This script takes as input two files containing non whitespace lines and will
+    output lines if it is present in both files.
+    """
+
+    # Set logging.
+    logging.basicConfig(
+        format="\n" + "=" * 55 + "\n%(asctime)s - %(levelname)s\n" + "=" * 55 + "\n%(message)s\n\n",
+        level=logging.DEBUG,
+    )
+
+    # Debug print.
+    ppp = pprint.PrettyPrinter(width=55)
+    prog_name = os.path.basename(inspect.stack()[0].filename)
+
+    parser = argparse.ArgumentParser(
+        prog=prog_name, description=main.__doc__, formatter_class=MultiArgFormatClasses
+    )
+
+    required = parser.add_argument_group("required arguments")
+
+    required.add_argument(
+        "-f1",
+        dest="file1",
+        default=False,
+        required=True,
+        help="Absolute UNIX path to file no. 1 containing\nnon white space lines.",
+    )
+    required.add_argument(
+        "-f2",
+        dest="file2",
+        default=False,
+        required=True,
+        help="Absolute UNIX path to file no. 2 containing\nnon white space lines.",
+    )
+    parser.add_argument(
+        "-out",
+        dest="outfile",
+        default="accs_passed.txt",
+        help="The following output file will be created in\nthe current working directory.",
+    )
+
+    args = parser.parse_args()
+    f1 = args.file1
+    f2 = args.file2
+    out = args.outfile
+    f1d = dict()
+    f2d = dict()
+
+    # Basic checks
+
+    if not (os.path.exists(f1) and os.path.exists(f2)):
+        logging.error(
+            f"File {os.path.basename(f1)} or" + f"\nFile {os.path.basename(f2)} does not exist."
+        )
+        exit(1)
+    elif not (os.path.getsize(f1) > 0 and os.path.getsize(f2) > 0):
+        logging.error(
+            f"File {os.path.basename(f1)} or" + f"\nFile {os.path.basename(f2)} is empty."
+        )
+        exit(1)
+
+    with open(f1, "r") as f1_fh:
+        for line in f1_fh:
+            f1d[line.strip()] = 1
+
+    with open(f2, "r") as f2_fh:
+        for line in f2_fh:
+            f2d[line.strip()] = 1
+
+    big = f1d
+    small = f2d
+
+    if len(f1d.keys()) < len(f2d.keys()):
+        big = f2d
+        small = f1d
+
+    with open(out, "w") as out_fh:
+        for line in small.keys():
+            if line in big.keys():
+                out_fh.write(line + "\n")
+
+    f1_fh.close()
+    f2_fh.close()
+    out_fh.close()
+
+
+if __name__ == "__main__":
+    main()