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annotate aggregate_gd_indivs.py @ 36:51cd0307fb70

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Phylip's extra ouputs are now stored in the job working directory
author Richard Burhans <burhans@bx.psu.edu>
date Wed, 20 Nov 2013 16:32:01 -0500
parents 8997f2ca8c7a
children
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1 #!/usr/bin/env python
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3 import gd_util
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4 import sys
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5 from Population import Population
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6
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7 ################################################################################
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9 if len(sys.argv) != 6:
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10 gd_util.dir('Usage')
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12 input, p1_input, output, input_type, ind_arg = sys.argv[1:]
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14 p_total = Population()
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15 p_total.from_wrapped_dict(ind_arg)
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17 p1 = Population()
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18 p1.from_population_file(p1_input)
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20 if not p_total.is_superset(p1):
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21 gd_util.die('There is an individual in the population that is not in the SNP table')
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23 ################################################################################
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25 prog = 'aggregate'
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27 args = [ prog ]
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28 args.append(input)
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30 if input_type == 'gd_snp':
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31 args.append(1)
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32 elif input_type == 'gd_genotype':
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33 args.append(0)
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34 else:
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35 die('unknown input type: {0}'.format(input_type))
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37 columns = p1.column_list()
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39 for column in sorted(columns):
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40 if input_type == 'gd_genotype':
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41 column = str(int(column) - 2)
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42 args.append(column)
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44 with open(output, 'w') as fh:
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45 gd_util.run_program(prog, args, stdout=fh)
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47 sys.exit(0)
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