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annotate diversity_pi.py @ 30:4188853b940b

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Update to Miller Lab devshed revision eb4e61d024db
author Richard Burhans <burhans@bx.psu.edu>
date Fri, 26 Jul 2013 12:51:13 -0400
parents 8997f2ca8c7a
children a631c2f6d913
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248b06e86022 Added gd_genotype datatype. Modified tools to support new datatype.
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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) != 7:
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10 gd_util.die('Usage')
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12 snp_input, coverage_input, indiv_input, min_coverage, output, 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(indiv_input)
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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 = 'mt_pi'
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26 args = [ prog ]
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27 args.append(snp_input)
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28 args.append(coverage_input)
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29 args.append(min_coverage)
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31 for tag in p1.tag_list():
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32 args.append(tag)
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34 with open(output, 'w') as fh:
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35 gd_util.run_program(prog, args, stdout=fh)
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37 sys.exit(0)
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