Mercurial > repos > miller-lab > genome_diversity

annotate draw_variants.py @ 27:8997f2ca8c7a

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Update to Miller Lab devshed revision bae0d3306d3b
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 15 Jul 2013 10:47:35 -0400
parents 248b06e86022
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) != 10:
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10 gd_util.die('Usage')
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12 snp_input, indel_input, coverage_input, annotation_input, indiv_input, ref_name, 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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23
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24 prog = 'mk_Ji'
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25
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26 args = [ prog ]
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27 args.append(snp_input)
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28 args.append(indel_input)
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29 args.append(coverage_input)
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30 args.append(annotation_input)
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31 args.append(min_coverage)
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32 args.append(ref_name)
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33
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34 for tag in p1.tag_list():
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35 args.append(tag)
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37 with open('mk_Ji.out', 'w') as fh:
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38 gd_util.run_program(prog, args, stdout=fh)
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39
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40 ################################################################################
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41
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42 prog = 'varplot'
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44 args = [ prog ]
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45 args.append('-w')
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46 args.append(3)
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47 args.append('-s')
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48 args.append(0.3)
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49 args.append('-g')
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50 args.append(0.2)
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51 args.append('mk_Ji.out')
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53 with open(output, 'w') as fh:
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54 gd_util.run_program(prog, args, stdout=fh)
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56 sys.exit(0)