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1 #!/usr/bin/env python
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2
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3 # <command interpreter="python">
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4 # add_fst_column.py "$input" "$p1_input" "$p2_input" "$data_source.choice" "$data_source.min_value" "$retain" "$discard_fixed" "$biased" "$output"
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5 # #for $individual, $individual_col in zip($input.dataset.metadata.individual_names, $input.dataset.metadata.individual_columns)
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6 # #set $arg = '%s:%s' % ($individual_col, $individual)
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7 # "$arg"
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8 # #end for
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9 # </command>
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10
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11 import sys
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12 import subprocess
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13 from Population import Population
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14
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15 ################################################################################
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16
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17 if len(sys.argv) < 12:
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18 print >> sys.stderr, "Usage"
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19 sys.exit(1)
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20
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21 input, p1_input, p2_input, genotypes, min_reads, min_qual, retain, discard_fixed, biased, output = sys.argv[1:11]
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22 individual_metadata = sys.argv[11:]
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23
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24 p_total = Population()
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25 p_total.from_tag_list(individual_metadata)
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26
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27 p1 = Population()
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28 p1.from_population_file(p1_input)
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29 if not p_total.is_superset(p1):
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30 print >> sys.stderr, 'There is an individual in population 1 that is not in the SNP table'
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31 sys.exit(1)
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32
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33 p2 = Population()
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34 p2.from_population_file(p2_input)
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35 if not p_total.is_superset(p2):
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36 print >> sys.stderr, 'There is an individual in population 2 that is not in the SNP table'
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37 sys.exit(1)
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38
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39 ################################################################################
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40
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41 prog = 'Fst_column'
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42
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43 args = []
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44 args.append(prog)
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45 args.append(input)
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46 args.append(genotypes)
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47 args.append(min_reads)
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48 args.append(min_qual)
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49 args.append(retain)
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50 args.append(discard_fixed)
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51 args.append(biased)
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52
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53 columns = p1.column_list()
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54 for column in columns:
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55 args.append('{0}:1'.format(column))
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56
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57 columns = p2.column_list()
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58 for column in columns:
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59 args.append('{0}:2'.format(column))
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60
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61 fh = open(output, 'w')
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62
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63 #print "args:", ' '.join(args)
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64 p = subprocess.Popen(args, bufsize=-1, stdin=None, stdout=fh, stderr=sys.stderr)
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65 rc = p.wait()
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66 fh.close()
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67
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68 sys.exit(0)
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69
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