Mercurial > repos > mvdbeek > add_input_name_as_column

annotate add_input_name_as_column.py @ 6:3284b72eef56 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
6
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
1 import argparse
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
2 import io
0
3a1f8302302d Imported from capsule None
mvdbeek
parents:
diff changeset
3
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
4
0
3a1f8302302d Imported from capsule None
mvdbeek
parents:
diff changeset
5 def Parser():
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
6 the_parser = argparse.ArgumentParser(description="add label to last column of file")
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
7 the_parser.add_argument('--input', required=True, action="store", type=str, help="input tabular file")
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
8 the_parser.add_argument('--output', required=True, action="store", type=str, help="output file path")
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
9 the_parser.add_argument('--label', required=True, action="store", type=str, help="label to add in last column")
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
10 the_parser.add_argument('--header', action="store", type=str, help="column label for last column")
6
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
11 the_parser.add_argument('--prepend', action='store_true', default=False, help='Prepend column instead of appending' )
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
12
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
13 args = the_parser.parse_args()
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
14 return args
0
3a1f8302302d Imported from capsule None
mvdbeek
parents:
diff changeset
15
3a1f8302302d Imported from capsule None
mvdbeek
parents:
diff changeset
16
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
17 args = Parser()
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
18
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
19
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
20 with io.open(args.input, encoding="utf-8") as input, io.open(args.output, 'w', encoding="utf-8") as output:
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
21 for i, line in enumerate(input):
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
22 line = line.strip('\n')
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
23 if (i == 0) and args.header:
6
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
24 new_entry = args.header
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
25 else:
6
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
26 new_entry = args.label
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
27 if args.prepend:
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
28 line = "%s\t%s\n" % (new_entry, line)
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
29 else:
3284b72eef56 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column commit 9292c57c34283543e86ecc65f805977224f6fc7b"
iuc
parents: 5
diff changeset
30 line = "%s\t%s\n" % (line, new_entry)
5
06061aa49527 planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/add_input_name_as_column commit db90fc6943b99322a6d7459f644a6624c69a0be5-dirty
mvdbeek
parents: 0
diff changeset
31 output.write(line)