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1 #!/usr/bin/env python
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2
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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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6
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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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12
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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
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16 p_total = Population()
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17 p_total.from_tag_list(individual_metadata)
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18
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19 p1 = Population()
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20 p1.from_population_file(p1_input)
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21
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22 if not p_total.is_superset(p1):
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23 print >> sys.stderr, 'There is an individual in the population that is not in the SNP table'
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24 sys.exit(1)
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25
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26 ################################################################################
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27
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28 prog = 'pop'
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29
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30 args = []
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31 args.append(prog)
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32 args.append(input)
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33 args.append(lo)
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34 args.append(hi)
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35 args.append(lo_ind)
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36 args.append(lo_ind_qual)
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37
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38 columns = p1.column_list()
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39
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40 for column in sorted(columns):
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41 args.append(column)
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42
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43 fh = open(output, 'w')
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44
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45 #print "args:", ' '.join(args)
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46 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
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47 rc = p.wait()
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48 fh.close()
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49
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50 sys.exit(0)
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51
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