Mercurial > repos > miller-lab > genome_diversity

annotate aggregate_gd_indivs.py @ 24:248b06e86022

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Added gd_genotype datatype. Modified tools to support new datatype.
author Richard Burhans <burhans@bx.psu.edu>
date Tue, 28 May 2013 16:24:19 -0400
parents 95a05c1ef5d5
children 91e835060ad2
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1 #!/usr/bin/env python
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3 import sys
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4 import subprocess
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5 from Population import Population
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7 ################################################################################
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8
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9 if len(sys.argv) < 9:
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10 print >> sys.stderr, "Usage"
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11 sys.exit(1)
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13 #input, p1_input, output, lo, hi, lo_ind, lo_ind_qual = sys.argv[1:8]
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14 #individual_metadata = sys.argv[8:]
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15 input, p1_input, output, = sys.argv[1:4]
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16 individual_metadata = sys.argv[4:]
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18 p_total = Population()
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19 p_total.from_tag_list(individual_metadata)
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21 p1 = Population()
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22 p1.from_population_file(p1_input)
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24 if not p_total.is_superset(p1):
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25 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
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26 sys.exit(1)
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28 ################################################################################
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29
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30 prog = 'aggregate'
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31
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32 args = []
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33 args.append(prog)
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34 args.append(input)
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35
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36 columns = p1.column_list()
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37
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38 for column in sorted(columns):
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39 args.append(column)
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40
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41 fh = open(output, 'w')
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42
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43 #print "args:", ' '.join(args)
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44 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
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45 rc = p.wait()
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46 fh.close()
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48 sys.exit(0)
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