annotate galaxy-tools/biobank/tools/map_vid.py @ 0:ba6cf6ede027 draft default tip

Uploaded
author ric
date Wed, 28 Sep 2016 06:03:30 -0400
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
1 # BEGIN_COPYRIGHT
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
2 # END_COPYRIGHT
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
3
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
4 import sys
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
5 from bl.vl.app.kb_query.main import main as kb_query
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
6
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
7 def main(argv):
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
8 selected_column, new_column_name, input_file = argv[:3]
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
9 selected_column = int(selected_column) - 1
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
10 new_column_name = new_column_name.strip()
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
11
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
12 # with open(input_file) as f:
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
13 # l = f.readline().strip()
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
14 # Backport to 2.6
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
15 fi = open(input_file)
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
16 l = fi.readline().strip()
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
17 fi.close()
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
18
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
19 column_names = l.split('\t')
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
20 column_name = column_names[selected_column]
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
21
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
22 argv = argv[3:] + ['--column=%s,%s' % (column_name, new_column_name)]
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
23 kb_query(argv)
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
24
ba6cf6ede027 Uploaded
ric
parents:
diff changeset
25 main(sys.argv[1:])