--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/ecoli_serotyping/commandLineOptions.py	Fri Jan 05 15:43:14 2018 -0500
@@ -0,0 +1,85 @@
+#!/usr/bin/env python
+
+import argparse
+
+
+def parse_command_line(args=None):
+    """
+    The options for both the serotyper, and virulence finder.
+    The returned object is used by both, but the options do not
+    necessarily apply to both.
+
+    Args:
+        args: Optional args to be passed to argparse.parse_args()
+
+    Returns:
+        The populated argparse Namespace
+    """
+
+    def check_percentage(value):
+        """
+        type checker for percentage input
+        """
+        ivalue = int(value)
+        if ivalue <= 0 or ivalue > 100:
+            raise argparse.ArgumentTypeError(
+                "{0} is an invalid positive int percentage value".format(value)
+            )
+        return ivalue
+
+    parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "-i",
+        "--input",
+        help="Location of new file(s). Can be a single file or \
+            a directory",
+        required=True
+    )
+
+    parser.add_argument(
+        "-d",
+        "--percentIdentity",
+        type=check_percentage,
+        help="Percentage of identity wanted to use against the\
+                  database. From 0 to 100, default is 90%%.",
+        default=90
+    )
+
+    parser.add_argument(
+        "-l",
+        "--percentLength",
+        type=check_percentage,
+        help="Percentage of length wanted to use against the \
+                  database. From 0 to 100, default is 50%%.",
+        default=50
+    )
+
+    parser.add_argument(
+        "--verify",
+        action="store_true",
+        help="Enable E. Coli. verification"
+    )
+
+    parser.add_argument(
+        "-s",
+        "--species",
+        action="store_true",
+        help="Enable species identification when non-ecoli genome is found\n\
+            Note: refseq downloading is required when running this option for the first time."
+    )
+
+    parser.add_argument(
+        '--detailed',
+        action='store_true',
+        help='Enable detailed output'
+    )
+
+    parser.add_argument(
+        "-o",
+        "--output",
+        help="Directory location of output files."
+    )
+
+    if args is None:
+        return parser.parse_args()
+    return parser.parse_args(args)