--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/auto_collapse_pop/auto_collapse_pops.py	Mon Feb 27 12:14:29 2017 -0500
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+
+######################################################################
+#                  Copyright (c) 2016 Northrop Grumman.
+#                          All rights reserved.
+######################################################################
+from __future__ import print_function
+import sys
+import pandas as pd
+from argparse import ArgumentParser
+
+
+def auto_collapse(input_file, profile_file, output, report):
+    profile_pop_list = {}
+    pop_to_collapse = []
+    markers = []
+    with open(profile_file, "r") as pf:
+        pffl = pf.readline()
+        markers = pffl.strip().split("\t")
+        for pfline in pf:
+            line = pfline.strip().split("\t")
+            pop = line[0]
+            profil = "\t".join(line[1:-2])
+            if profil in profile_pop_list:
+                profile_pop_list[profil].append(pop)
+            else:
+                profile_pop_list[profil] = [pop]
+    i = 1
+    with open(report, "w") as rt:
+        rt.write("New_Population\tFormer_Populations\t")
+        rt.write("\t".join(markers[1:-2]) + "\n")
+        for profs in profile_pop_list:
+            pop_to_collapse.append(profile_pop_list[profs])
+            pop_ls = ", ".join(profile_pop_list[profs])
+            rt.write("\t".join([str(i), pop_ls, profs]) + "\n")
+            i += 1
+    df = pd.read_table(input_file, dtype={'Population': object})
+    df['new_population'] = df.Population
+    for i, sets_pop in enumerate(pop_to_collapse):
+        df.loc[df['Population'].isin(sets_pop), ['new_population']] = i + 1
+
+    df.Population = df.new_population
+    df.drop(['new_population'], inplace=True, axis=1)
+    df.to_csv(output, sep="\t", index=False)
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="auto_pop_collapse_from_profile",
+             description="collapses FLOCK populations based on profile.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_file",
+            required=True,
+            help="FLOCK output file")
+
+    parser.add_argument(
+            '-o',
+            dest="output",
+            required=True,
+            help="Name of the output file.")
+
+    parser.add_argument(
+            '-r',
+            dest="report",
+            required=True,
+            help="Name of the report file.")
+
+    parser.add_argument(
+            '-p',
+            dest="profile",
+            required=True,
+            help="File location for the profile.txt from FLOCK.")
+
+    args = parser.parse_args()
+
+    auto_collapse(args.input_file, args.profile, args.output, args.report)
+    sys.exit(0)