--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/application.py	Thu Oct 15 07:45:17 2020 +0000
@@ -0,0 +1,66 @@
+import argparse
+
+import psmfragmentation.psmfragmentation as pf
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(description="Run PSM Validator")
+    parser.add_argument(
+        "-d",
+        "--dbname",
+        help="Path to mzsqlite db",
+    )
+    parser.add_argument(
+        "-p",
+        "--peptides",
+        help="Path to peptide sequence file",
+    )
+    parser.add_argument(
+        "-n",
+        "--neutral",
+        action="store_true",
+        default=False,
+        help="Calculate netutral loss",
+    )
+    parser.add_argument(
+        "-i",
+        "--internal",
+        action="store_true",
+        default=False,
+        help="Calculate internals",
+    )
+    parser.add_argument(
+        "-e", "--epsilon", type=float
+    )
+    parser.add_argument(
+        "-b",
+        "--b_run",
+        type=int,
+        default=2,
+        help="Number of consecutive b-ions"
+    )
+    parser.add_argument(
+        "-y",
+        "--y_run",
+        type=int,
+        default=2,
+        help="Number of consecutive y-ions"
+    )
+
+    parser.add_argument(
+        "-t",
+        "--test",
+        action="store_true",
+        default=False
+    )
+
+    args = parser.parse_args()
+
+    itypes = ['b', 'y']
+    if args.neutral:
+        itypes.extend(['b-H2O', 'b-NH3', 'y-H2O', 'y-NH3'])
+
+    if args.internal:
+        itypes.append('M')
+
+    pf.score_psms(args.dbname, args.peptides, ion_types=itypes, epsilon=args.epsilon, maxcharge=1, b_run=args.b_run, y_run=args.y_run, a_test=args.test)