Mercurial > repos > immport-devteam > collapse_pop

comparison collapse_pops.py @ 1:a3ae90eb1232 draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/collapse_pop commit 1e75b0df5680c0cdd8b2b3e5d4c1f8077b430944"
author azomics
date Mon, 22 Jun 2020 16:34:35 -0400
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0:59f859ea3122 1:a3ae90eb1232
1 #!/usr/bin/env python
2 ######################################################################
3 # Copyright (c) 2016 Northrop Grumman.
4 # All rights reserved.
5 ######################################################################
6
7 from __future__ import print_function
8 import sys
9 import pandas as pd
10
11 from argparse import ArgumentParser
12
13
14 def is_int(s):
15 try:
16 int(s)
17 return True
18 except ValueError:
19 return False
20
21
22 def collapse_populations(in_file, out_file, populations, collapse_in, exit_code):
23 df = pd.read_table(in_file, dtype={'Population': object})
24 df['new_population'] = df.Population
25
26 for i, sets_pop in enumerate(populations):
27 df.loc[df['Population'].isin(sets_pop), ['new_population']] = collapse_in[i]
28
29 df.Population = df.new_population
30 df.drop(['new_population'], inplace=True, axis=1)
31
32 df.to_csv(out_file, sep="\t", index=False)
33
34 sys.exit(exit_code)
35
36
37 if __name__ == "__main__":
38 parser = ArgumentParser(
39 prog="ExtractPop",
40 description="Extract events associated to given population numbers.")
41
42 parser.add_argument(
43 '-i',
44 dest="input_file",
45 required=True,
46 help="File location for the text file.")
47
48 parser.add_argument(
49 '-p',
50 dest="pops",
51 required=True,
52 action='append',
53 help="List of populations to collapse.")
54
55 parser.add_argument(
56 '-o',
57 dest="output_file",
58 required=True,
59 help="Name of the output file.")
60
61 parser.add_argument(
62 '-c',
63 dest="collapse_pop",
64 required=True,
65 action='append',
66 help="What to collapse the populations in.")
67
68 args = parser.parse_args()
69
70 # check populations
71 default_values_pop = ["i.e.:2,3,11,25", "default", "Default"]
72 default_values_col = ["i.e.:4", "default", "Default"]
73 pops = [p for p in args.pops]
74 popc = [pc.strip() for pc in args.collapse_pop]
75 exit_code = 0
76 # Check sets of pops to collapse
77 populations = []
78 total_pops = []
79 for pop_set in pops:
80 if pop_set not in default_values_pop:
81 tmp_pops = pop_set.split(",")
82 for popn in tmp_pops:
83 if not is_int(popn):
84 sys.exit(6)
85 else:
86 total_pops.append(int(popn))
87 strp_pops = [p.strip() for p in tmp_pops]
88 populations.append(strp_pops)
89 else:
90 sys.exit(4)
91 if len(total_pops) != len(set(total_pops)):
92 sys.exit(7)
93 # Check pops to collapse in
94 collapse_in = []
95 for col_pop in popc:
96 if col_pop not in default_values_col:
97 if not is_int(col_pop):
98 sys.exit(6)
99 else:
100 if int(col_pop) > 40:
101 exit_code = 2
102 collapse_in.append(col_pop)
103 else:
104 sys.exit(6)
105 if len(collapse_in) != len(set(collapse_in)):
106 exit_code += 3
107
108 collapse_populations(args.input_file, args.output_file, populations, collapse_in, exit_code)