diff collapse_pops.py @ 1:a3ae90eb1232 draft default tip

"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/collapse_pop commit 1e75b0df5680c0cdd8b2b3e5d4c1f8077b430944"

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/collapse_pops.py	Mon Jun 22 16:34:35 2020 -0400
@@ -0,0 +1,108 @@
+#!/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 collapse_populations(in_file, out_file, populations, collapse_in, exit_code):
+    df = pd.read_table(in_file, dtype={'Population': object})
+    df['new_population'] = df.Population
+
+    for i, sets_pop in enumerate(populations):
+        df.loc[df['Population'].isin(sets_pop), ['new_population']] = collapse_in[i]
+
+    df.Population = df.new_population
+    df.drop(['new_population'], inplace=True, axis=1)
+
+    df.to_csv(out_file, sep="\t", index=False)
+
+    sys.exit(exit_code)
+
+
+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,
+            action='append',
+            help="List of populations to collapse.")
+
+    parser.add_argument(
+            '-o',
+            dest="output_file",
+            required=True,
+            help="Name of the output file.")
+
+    parser.add_argument(
+            '-c',
+            dest="collapse_pop",
+            required=True,
+            action='append',
+            help="What to collapse the populations in.")
+
+    args = parser.parse_args()
+
+    # check populations
+    default_values_pop = ["i.e.:2,3,11,25", "default", "Default"]
+    default_values_col = ["i.e.:4", "default", "Default"]
+    pops = [p for p in args.pops]
+    popc = [pc.strip() for pc in args.collapse_pop]
+    exit_code = 0
+    # Check sets of pops to collapse
+    populations = []
+    total_pops = []
+    for pop_set in pops:
+        if pop_set not in default_values_pop:
+            tmp_pops = pop_set.split(",")
+            for popn in tmp_pops:
+                if not is_int(popn):
+                    sys.exit(6)
+                else:
+                    total_pops.append(int(popn))
+            strp_pops = [p.strip() for p in tmp_pops]
+            populations.append(strp_pops)
+        else:
+            sys.exit(4)
+    if len(total_pops) != len(set(total_pops)):
+        sys.exit(7)
+    # Check pops to collapse in
+    collapse_in = []
+    for col_pop in popc:
+        if col_pop not in default_values_col:
+            if not is_int(col_pop):
+                sys.exit(6)
+            else:
+                if int(col_pop) > 40:
+                    exit_code = 2
+                collapse_in.append(col_pop)
+        else:
+            sys.exit(6)
+    if len(collapse_in) != len(set(collapse_in)):
+        exit_code += 3
+
+    collapse_populations(args.input_file, args.output_file, populations, collapse_in, exit_code)