Mercurial > repos > miller-lab > genome_diversity

annotate nucleotide_diversity_pi.py @ 29:fb944979bf35

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Update to Miller Lab devshed revision 5f0be4d1db30
author Richard Burhans <burhans@bx.psu.edu>
date Thu, 25 Jul 2013 12:01:47 -0400
parents 8997f2ca8c7a
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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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7 ################################################################################
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9 if len(sys.argv) != 7:
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10 gd_util.die('Usage')
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12 gd_saps_file, gd_snps_file, covered_intervals_file, gd_indivs_file, output_file, 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(gd_indivs_file)
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19 if not p_total.is_superset(p1):
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20 gd_util.die('There is an individual in the population individuals that is not in the SNP table')
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22 ################################################################################
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24 prog = 'get_pi'
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26 args = [ prog ]
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27 args.append(gd_saps_file)
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28 args.append(gd_snps_file)
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29 args.append(covered_intervals_file)
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31 columns = p1.column_list()
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32 for column in columns:
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33 args.append(column)
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35 with open(output_file, 'w') as fh:
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36 gd_util.run_program(prog, args, stdout=fh)
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38 sys.exit(0)
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