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annotate diversity_pi.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 a631c2f6d913
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 def load_pop(file, wrapped_dict):
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10 if file == '/dev/null':
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11 pop = None
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12 else:
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13 pop = Population()
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14 pop.from_wrapped_dict(wrapped_dict)
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15 return pop
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17 def append_tags(the_list, p, p_type, val):
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18 if p is None:
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19 return
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20 for tag in p.tag_list():
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21 column, name = tag.split(':')
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22 if p_type == 'gd_genotype':
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23 column = int(column) - 2
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24 the_list.append('{0}:{1}:{2}'.format(val, column, name))
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26 ################################################################################
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28 if len(sys.argv) != 11:
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29 gd_util.die('Usage')
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31 snp_input, snp_ext, snp_arg, cov_input, cov_ext, cov_arg, indiv_input, min_coverage, req_thresh, output = sys.argv[1:]
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33 p_snp = load_pop(snp_input, snp_arg)
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34 p_cov = load_pop(cov_input, cov_arg)
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35
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36 p_ind = Population()
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37 p_ind.from_population_file(indiv_input)
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38
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39 if not p_snp.is_superset(p_ind):
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40 gd_util.die('There is an individual in the population individuals that is not in the SNP/Genotype table')
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42 if p_cov is not None and (not p_cov.is_superset(p_ind)):
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43 gd_util.die('There is an individual in the population individuals that is not in the Coverage table')
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45 ################################################################################
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47 prog = 'mito_pi'
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49 args = [ prog ]
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50 args.append(snp_input)
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51 args.append(cov_input)
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52 args.append(min_coverage)
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53 args.append(req_thresh)
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55 append_tags(args, p_ind, 'gd_indivs', 0)
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56 append_tags(args, p_snp, snp_ext, 1)
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57 append_tags(args, p_cov, cov_ext, 2)
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59 with open(output, 'w') as fh:
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60 gd_util.run_program(prog, args, stdout=fh)
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62 sys.exit(0)
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