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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) < 12:
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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, p2_input, data_source, min_total_count, discard_fixed, biased, output, shuffles, p0_input = sys.argv[1:11]
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14 individual_metadata = sys.argv[11:]
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15
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16 try:
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17 shuffle_count = int(shuffles)
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18 except:
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19 shuffle_count = 0
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20
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21 p_total = Population()
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22 p_total.from_tag_list(individual_metadata)
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23
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24 p1 = Population()
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25 p1.from_population_file(p1_input)
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26 if not p_total.is_superset(p1):
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27 print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table'
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28 sys.exit(1)
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29
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30 p2 = Population()
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31 p2.from_population_file(p2_input)
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32 if not p_total.is_superset(p2):
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33 print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table'
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34 sys.exit(1)
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35
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36 p0 = None
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37 if shuffle_count > 0:
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38 p0 = Population()
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39 p0.from_population_file(p0_input)
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40 if not p_total.is_superset(p0):
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41 print >> sys.stderr, 'There is an individual in population 0 that is not in the SNP table'
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42 sys.exit(1)
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43
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44 ################################################################################
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45
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46 prog = 'Fst_ave'
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47
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48 args = []
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49 args.append(prog)
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50 args.append(input)
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51 args.append(data_source)
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52 args.append(min_total_count)
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53 args.append(discard_fixed)
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54 args.append(biased)
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55 args.append(shuffles)
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56
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57 columns = p1.column_list()
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58 for column in columns:
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59 args.append('{0}:1'.format(column))
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60
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61 columns = p2.column_list()
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62 for column in columns:
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63 args.append('{0}:2'.format(column))
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64
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65 if p0 is not None:
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66 columns = p0.column_list()
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67 for column in columns:
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68 args.append('{0}:0'.format(column))
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69
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70 fh = open(output, 'w')
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71
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72 #print "args:", ' '.join(args)
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73 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
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74 rc = p.wait()
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75 fh.close()
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76
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77 sys.exit(0)
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78
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