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10
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1 #!/usr/bin/env python
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2 import os
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3 import sys
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4 import subprocess
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5
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6 DATASETS = [
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7 'artificial',
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8 'artificial-samples',
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9 'artificial-nofilt',
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10 'real',
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11 'real-mit',
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12 'real-mit-s',
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13 'real-nofilt',
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14 ]
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15 IN_EXT = '.vcf.in'
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16 OUT_EXT = '.csv.out'
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17 ARGS_KEY = '##comment="ARGS='
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18
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11
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19 XML = {
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20 'tests_start':' <tests>',
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21 'test_start': ' <test>',
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22 'input': ' <param name="input" value="tests/%s" />',
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23 'param': ' <param name="%s" value="%s" />',
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24 'output': ' <output name="output" file="tests/%s" />',
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25 'test_end': ' </test>',
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26 'tests_end': ' </tests>',
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27 }
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28 PARAMS = {
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29 '-f':'freq',
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30 '-c':'covg',
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31 '-H':'header',
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32 '-s':'stranded',
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33 '-n':'nofilt',
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34 '-r':'seed',
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35 }
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36 PARAM_ARG = {
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37 '-f':True,
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38 '-c':True,
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39 '-H':False,
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40 '-s':False,
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41 '-n':False,
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42 '-r':True,
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43 }
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44
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10
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45 def main():
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46
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11
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47 do_print_xml = False
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48 if len(sys.argv) > 1:
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49 if sys.argv[1] == '-x':
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50 do_print_xml = True
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51 else:
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52 sys.stderr.write("Error: unrecognized option '"+sys.argv[1]+"'\n")
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53 sys.exit(1)
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54
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10
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55 test_dir = os.path.dirname(os.path.relpath(sys.argv[0]))
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56 if test_dir:
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57 test_dir += os.sep
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58
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11
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59 if do_print_xml:
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60 print XML.get('tests_start')
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61
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10
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62 for dataset in DATASETS:
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63 infile = test_dir+dataset+IN_EXT
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64 outfile = test_dir+dataset+OUT_EXT
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65
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66 if not os.path.exists(infile):
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67 sys.stderr.write("Error: file not found: "+infile+"\n")
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68 continue
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69 if not os.path.exists(outfile):
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70 sys.stderr.write("Error: file not found: "+outfile+"\n")
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71 continue
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72
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73 options = read_options(infile)
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11
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74 if do_print_xml:
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75 print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
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76 else:
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77 run_tests(infile, outfile, options)
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78
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79 if do_print_xml:
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80 print XML.get('tests_end')
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81
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82
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83 def run_tests(infile, outfile, options):
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84 script_cmd = 'allele-counts.py '+options+' -i '+infile
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85 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
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86 print script_cmd
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87 subprocess.call(['bash', '-c', bash_cmd])
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88
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89
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90 def print_xml(infile, outfile, options_str, xml, params, param_arg):
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91 infile = os.path.basename(infile)
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92 outfile = os.path.basename(outfile)
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93
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94 options = options_str.split() # on whitespace
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95
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96 print xml.get('test_start')
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97 print xml.get('input') % infile
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98
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99 i = 0
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100 while i < len(options):
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101 opt = options[i]
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102 if not params.has_key(opt) or not param_arg.has_key(opt):
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103 sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "
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104 +infile+"\n")
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105 sys.exit(1)
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106 if param_arg[opt]:
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107 i+=1
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108 arg = options[i]
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109 print xml.get('param') % (params[opt], arg)
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110 else:
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111 print xml.get('param') % (params[opt], opt)
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112 i+=1
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113
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114 print xml.get('output') % outfile
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115 print xml.get('test_end')
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10
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116
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117
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118 def read_options(infile):
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119 with open(infile, 'r') as infilehandle:
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120 for line in infilehandle:
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121 line.strip()
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122 if ARGS_KEY == line[:len(ARGS_KEY)]:
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123 return line[len(ARGS_KEY):-2]
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124 return ''
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125
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126
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127 if __name__ == '__main__':
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128 main() |
