Mercurial > repos > pieterlukasse > prims_metabolomics
comparison select_on_rank.py @ 0:9d5f4f5f764b
Initial commit to toolshed
| author | pieter.lukasse@wur.nl |
|---|---|
| date | Thu, 16 Jan 2014 13:10:00 +0100 |
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| children |
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| -1:000000000000 | 0:9d5f4f5f764b |
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| 1 import csv | |
| 2 import sys | |
| 3 | |
| 4 __author__ = "Marcel Kempenaar" | |
| 5 __contact__ = "brs@nbic.nl" | |
| 6 __copyright__ = "Copyright, 2012, Netherlands Bioinformatics Centre" | |
| 7 __license__ = "MIT" | |
| 8 | |
| 9 in_file = sys.argv[1] | |
| 10 out_file = sys.argv[2] | |
| 11 to_select_list = [str(select.strip()) for select in sys.argv[3].split(',') if (len(select) > 0)] | |
| 12 | |
| 13 data = list(csv.reader(open(in_file, 'rb'), delimiter='\t')) | |
| 14 header = data.pop(0) | |
| 15 header_clean = [i.lower().strip().replace(".", "").replace("%", "") for i in header] | |
| 16 rank = header_clean.index("rank") | |
| 17 | |
| 18 writer = csv.writer(open(out_file, 'wb'), delimiter='\t') | |
| 19 writer.writerow(header) | |
| 20 for select in to_select_list: | |
| 21 writer.writerows([i for i in data if i[rank] == select]) |