Mercurial > repos > immport-devteam > txt_diagnosis
comparison txt_diagnosis/txtdiagnosis.py @ 0:e1f0194cf8fc draft
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author | immport-devteam |
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date | Mon, 27 Feb 2017 13:07:11 -0500 |
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-1:000000000000 | 0:e1f0194cf8fc |
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1 #!/usr/bin/env python | |
2 ###################################################################### | |
3 # Copyright (c) 2016 Northrop Grumman. | |
4 # All rights reserved. | |
5 ###################################################################### | |
6 from __future__ import print_function | |
7 from __future__ import division | |
8 import pandas as pd | |
9 from argparse import ArgumentParser | |
10 import sys | |
11 | |
12 | |
13 def is_number(s): | |
14 try: | |
15 float(s) | |
16 return True | |
17 except ValueError: | |
18 return False | |
19 | |
20 | |
21 def error_report(input_file, fname, output_file): | |
22 errors = 0 | |
23 df = pd.read_table(input_file) | |
24 with open(output_file, "w") as outf: | |
25 for cols in df.columns.values: | |
26 if df[cols].count() != len(df[cols]): | |
27 with open(input_file, "r") as checkfile: | |
28 fl = checkfile.readline() | |
29 count_lines = 1 | |
30 for checklines in checkfile: | |
31 to_check = checklines.strip().split("\t") | |
32 count_lines += 1 | |
33 for item in to_check: | |
34 if not is_number(item): | |
35 errors += 1 | |
36 outf.write(" ".join(["WARNING: line", str(count_lines), "in", fname, "contains non-numeric results\n"])) | |
37 if errors == 0: | |
38 outf.write("No errors in the file.\n") | |
39 return | |
40 | |
41 | |
42 if __name__ == "__main__": | |
43 parser = ArgumentParser( | |
44 prog="txtDiagnosis", | |
45 description="Reports potential errors in text-converted FCS files") | |
46 | |
47 parser.add_argument( | |
48 '-i', | |
49 dest="input_file", | |
50 required=True, | |
51 help="File location for the text file.") | |
52 | |
53 parser.add_argument( | |
54 '-n', | |
55 dest="filename", | |
56 required=True, | |
57 help="Filename location for the text file.") | |
58 | |
59 parser.add_argument( | |
60 '-o', | |
61 dest="output_file", | |
62 required=True, | |
63 help="Name of the output file.") | |
64 | |
65 args = parser.parse_args() | |
66 | |
67 error_report(args.input_file, args.filename, args.output_file) | |
68 sys.exit(0) |