Mercurial > repos > mvdbeek > add_input_name_as_column

comparison add_input_name_as_column.py @ 6:3284b72eef56 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
author iuc
date Wed, 25 Mar 2020 07:11:05 -0400
parents 06061aa49527
children 8061668d0868
comparison
equal deleted inserted replaced
5:06061aa49527 6:3284b72eef56
1 import argparse
1 import io 2 import io
2 import argparse
3 3
4 4
5 def Parser(): 5 def Parser():
6 the_parser = argparse.ArgumentParser(description="add label to last column of file") 6 the_parser = argparse.ArgumentParser(description="add label to last column of file")
7 the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file") 7 the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file")
8 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path") 8 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path")
9 the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column") 9 the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column")
10 the_parser.add_argument('--header', action="store", type=str, help="column label for last column") 10 the_parser.add_argument('--header', action="store", type=str, help="column label for last column")
11 the_parser.add_argument('--prepend', action='store_true', default=False, help='Prepend column instead of appending' )
12
11 args = the_parser.parse_args() 13 args = the_parser.parse_args()
12 return args 14 return args
13 15
14 16
15 args = Parser() 17 args = Parser()
17 19
18 with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output: 20 with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output:
19 for i, line in enumerate(input): 21 for i, line in enumerate(input):
20 line = line.strip('\n') 22 line = line.strip('\n')
21 if (i == 0) and args.header: 23 if (i == 0) and args.header:
22 line = "%s\t%s\n" % (line, args.header) 24 new_entry = args.header
23 else: 25 else:
24 line = "%s\t%s\n" % (line, args.label) 26 new_entry = args.label
27 if args.prepend:
28 line = "%s\t%s\n" % (new_entry, line)
29 else:
30 line = "%s\t%s\n" % (line, new_entry)
25 output.write(line) 31 output.write(line)