Mercurial > repos > immport-devteam > check_headers

comparison getHeaders.py @ 1:05440ef97f8b draft default tip

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"planemo upload for repository https://github.com/ImmPortDB/immport-galaxy-tools/tree/master/flowtools/check_headers commit 14d780f8710fb0962a85c262d0689a9551f4f8e1"
author azomics
date Tue, 14 Jul 2020 09:46:31 -0400
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0:e88c99a4fb36 1:05440ef97f8b
1 #!/usr/bin/env python
2 ######################################################################
3 # Copyright (c) 2016 Northrop Grumman.
4 # All rights reserved.
5 ######################################################################
6 #
7 # Version 1.2 - May 2018
8 # added leeway for files with different nb of headers
9 #
10
11
12 import sys
13
14 from argparse import ArgumentParser
15
16
17 def print_headers(files, filenames, outfile):
18 header_table = {}
19 for i, eachfile in enumerate(files):
20 with open(eachfile, "r") as ef:
21 headers = ef.readline().strip()
22 header_table[filenames[i]] = headers.split("\t")
23
24 h = 0
25 for f in header_table:
26 j = len(header_table[f]) + 1
27 if j > h:
28 h = j
29
30 idx = [str(x) for x in range(1, h)]
31
32 with open(outfile, "w") as outf:
33 outf.write("Index\t")
34 outf.write("\t".join(idx) + "\n")
35 for f in header_table:
36 if len(header_table[f]) < h:
37 for k in range(len(header_table[f]), h-1):
38 header_table[f].append("")
39 sys.stderr.write(str(len(header_table[f])))
40 outf.write(f + "\t")
41 outf.write("\t".join(header_table[f]) + "\n")
42 return
43
44
45 if __name__ == "__main__":
46 parser = ArgumentParser(
47 prog="GetHeaders",
48 description="Gets the headers of all files in given set.")
49
50 parser.add_argument(
51 '-i',
52 dest="input_files",
53 required=True,
54 action='append',
55 help="File location for the text files.")
56
57 parser.add_argument(
58 '-n',
59 dest="file_names",
60 required=True,
61 action='append',
62 help="File names.")
63
64 parser.add_argument(
65 '-o',
66 dest="output_file",
67 required=True,
68 help="Name of the output file.")
69
70 args = parser.parse_args()
71 input_files = [f for f in args.input_files]
72 file_names = [fn for fn in args.file_names]
73 print_headers(input_files, file_names, args.output_file)