diff extractpop.py @ 1:4f28ee74079b draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/extract_pop commit 117c0e4a5c00dfd2e190359badf77d5643fccefa"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/extractpop.py	Fri Jul 24 19:24:49 2020 -0400
@@ -0,0 +1,84 @@
+#!/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 is_int(s):
+    try:
+        int(s)
+        return True
+    except ValueError:
+        return False
+
+
+def extract_pop(in_file, pop_list, out_file):
+    df = pd.read_table(in_file, dtype={'Population': object})
+    dfout = df.loc[df['Population'].isin(pop_list)]
+    dfout.to_csv(out_file, sep="\t", index=False)
+    return
+
+
+def remove_pop(in_file, pop_list, out_file):
+    df = pd.read_table(in_file, dtype={'Population': object})
+    dfout = df.loc[~df['Population'].isin(pop_list)]
+    dfout.to_csv(out_file, sep="\t", index=False)
+    return
+
+
+if __name__ == "__main__":
+    parser = ArgumentParser(
+             prog="ExtractPop",
+             description="Extract events associated to given population numbers.")
+
+    parser.add_argument(
+            '-i',
+            dest="input_file",
+            required=True,
+            help="File location for the text file.")
+
+    parser.add_argument(
+            '-p',
+            dest="pops",
+            required=True,
+            help="List of populations to extract.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    parser.add_argument(
+            '-m',
+            dest="method",
+            required=True,
+            help="What to do with the populations.")
+
+    args = parser.parse_args()
+
+    # check populations
+    default_values = ["i.e.:2,3,11,25", "default", "Default"]
+    populations = []
+    if args.pops:
+        if args.pops not in default_values:
+            tmp_pops = args.pops.split(",")
+            for popn in tmp_pops:
+                populations.append(popn.strip())
+        else:
+            sys.exit(2)
+    for pops in populations:
+        if not is_int(pops):
+            sys.exit(3)
+    if args.method == "selected":
+        extract_pop(args.input_file, populations, args.output_file)
+    else:
+        remove_pop(args.input_file, populations, args.output_file)