Mercurial > repos > mvdbeek > add_input_name_as_column

comparison add_input_name_as_column.py @ 5:06061aa49527 draft

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planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
author mvdbeek
date Wed, 06 Mar 2019 09:16:29 -0500
parents 3a1f8302302d
children 3284b72eef56
comparison
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4:b31219f26a8f 5:06061aa49527
1 import sys 1 import io
2 import argparse 2 import argparse
3 3
4
4 def Parser(): 5 def Parser():
5 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")
6 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")
7 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")
8 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")
9 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")
10 args = the_parser.parse_args() 11 args = the_parser.parse_args()
11 return args 12 return args
12 13
13 args=Parser()
14 14
15 input=open(args.input) 15 args = Parser()
16 output=open(args.output, 'w') 16
17 for i,line in enumerate(input): 17
18 line=line.strip('\n') 18 with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output:
19 if (i==0) and (args.header!=None): 19 for i, line in enumerate(input):
20 line=line+'\t'+args.header 20 line = line.strip('\n')
21 else: 21 if (i == 0) and args.header:
22 line=line+'\t'+args.label 22 line = "%s\t%s\n" % (line, args.header)
23 print >>output, line 23 else:
24 input.close() 24 line = "%s\t%s\n" % (line, args.label)
25 output.close() 25 output.write(line)