Mercurial > repos > bgruening > column_arrange_by_header
comparison column_arrange.py @ 0:f18f67056946 draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit 088e73e958b55dc765778641b8a84080cc289f85-dirty
| author | bgruening |
|---|---|
| date | Fri, 16 Oct 2015 14:31:13 -0400 |
| parents | |
| children | 6c6d26ff01ff |
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| -1:000000000000 | 0:f18f67056946 |
|---|---|
| 1 #!/usr/bin/env python | |
| 2 import pandas as pd | |
| 3 import argparse | |
| 4 | |
| 5 parser = argparse.ArgumentParser() | |
| 6 parser.add_argument('-i', '--input', help='Tabular Input File Name') | |
| 7 parser.add_argument('-o','--output', help='Tabular Output File') | |
| 8 parser.add_argument('-c', '--columns', nargs='+', help='Column Headers to Sort By') | |
| 9 args=parser.parse_args() | |
| 10 | |
| 11 cols = args.columns | |
| 12 table = pd.read_csv(args.input, sep='\t') | |
| 13 blist = list(table.columns) | |
| 14 for token in cols: | |
| 15 blist.remove(token) | |
| 16 sorted_table = table[args.columns + blist] | |
| 17 # write without index, seperated by tabs | |
| 18 sorted_table.to_csv(args.output, sep='\t', index=False) |