annotate galaxy-tools/biobank/tools/map_vid.py @ 0:e54d14bed3f5 draft default tip

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author ric
date Thu, 29 Sep 2016 06:09:15 -0400
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1 # BEGIN_COPYRIGHT
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2 # END_COPYRIGHT
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3
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4 import sys
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5 from bl.vl.app.kb_query.main import main as kb_query
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6
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7 def main(argv):
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8 selected_column, new_column_name, input_file = argv[:3]
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9 selected_column = int(selected_column) - 1
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10 new_column_name = new_column_name.strip()
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11
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12 # with open(input_file) as f:
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13 # l = f.readline().strip()
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14 # Backport to 2.6
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15 fi = open(input_file)
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16 l = fi.readline().strip()
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17 fi.close()
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19 column_names = l.split('\t')
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20 column_name = column_names[selected_column]
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21
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22 argv = argv[3:] + ['--column=%s,%s' % (column_name, new_column_name)]
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23 kb_query(argv)
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24
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25 main(sys.argv[1:])