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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
author bgruening
date Fri, 15 Feb 2019 07:44:19 -0500
parents b97f0d9a31ff
children
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a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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1 #!/usr/bin/env python
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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3 import argparse
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4
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5 parser = argparse.ArgumentParser()
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6 parser.add_argument('-i', '--input', help='Tabular Input File Name')
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7 parser.add_argument('-o','--output', help='Tabular Output File')
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a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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8 parser.add_argument(
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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9 '-c', '--columns', nargs='+', help='Column Headers to Sort By'
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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10 )
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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11 parser.add_argument(
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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12 '-d', '--discard', action='store_true',
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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13 help='Discard remaining columns'
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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14 )
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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15
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16 args=parser.parse_args()
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17
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a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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18 with open(args.input) as data:
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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19 hdr = next(data)
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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20 columns = hdr.rstrip('\n').split('\t')
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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21 idx = [columns.index(name) for name in args.columns]
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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22 if not args.discard:
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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23 idx += [i for i in range(len(columns)) if i not in idx]
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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24 rearranged_cols = [columns[i] for i in idx]
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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25 with open(args.output, 'w') as out:
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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26 out.write('\t'.join(rearranged_cols) + '\n')
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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27 for line in data:
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
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28 columns = line.rstrip('\n').split('\t')
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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29 rearranged_cols = [columns[i] for i in idx]
a69463bf1801 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/text_processing/column_arrange_by_header commit b6e0b2de32ddb91085235397728623a35ad13f42
bgruening
parents: 1
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30 out.write('\t'.join(rearranged_cols) + '\n')