Mercurial > repos > nick > allele_counts

annotate tests/run-tests.py @ 11:cf2af5c3118c draft default tip

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"planemo upload for repository https://github.com/galaxyproject/dunovo commit ac9577f0047ad984b307fe2c4b40e2eb45a0e6e2"
author nick
date Fri, 03 Apr 2020 16:05:04 -0400
parents 6cc488e11544
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
9
6cc488e11544 "planemo upload for repository https://github.com/galaxyproject/dunovo commit 5a2e08bc1213b0437d0adcb45f7f431bd3c735f4"
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1 #!/usr/bin/env python3
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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 SCRIPT_NAME = 'allele-counts.py'
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7 DATASETS = [
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8 'artificial',
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9 'artificial-samples',
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10 'artificial-nofilt',
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11 'real',
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12 'real-mit',
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13 'real-mit-s',
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14 'real-nofilt',
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15 ]
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16 IN_EXT = '.vcf.in'
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17 OUT_EXT = '.csv.out'
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18 ARGS_KEY = '##comment="ARGS='
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19
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20 XML = {
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21 'tests_start':' <tests>',
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22 'test_start': ' <test>',
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23 'input': ' <param name="input" value="tests/%s" />',
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24 'param': ' <param name="%s" value="%s" />',
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25 'output': ' <output name="output" file="tests/%s" />',
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26 'test_end': ' </test>',
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27 'tests_end': ' </tests>',
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28 }
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29 PARAMS = {
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30 '-f':'freq',
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31 '-c':'covg',
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32 '-H':'header',
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33 '-s':'stranded',
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34 '-n':'nofilt',
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35 '-r':'seed',
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36 }
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37 PARAM_ARG = {
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38 '-f':True,
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39 '-c':True,
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40 '-H':False,
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41 '-s':False,
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42 '-n':False,
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43 '-r':True,
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44 }
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45
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46 def main():
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47
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48 do_print_xml = False
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49 if len(sys.argv) > 1:
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50 if sys.argv[1] == '-x':
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51 do_print_xml = True
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52 else:
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53 sys.stderr.write("Error: unrecognized option '"+sys.argv[1]+"'\n")
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54 sys.exit(1)
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55
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56 test_dir = os.path.dirname(os.path.realpath(__file__))
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57 script_dir = os.path.relpath(os.path.dirname(test_dir))
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58 test_dir = os.path.relpath(test_dir)
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59
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60 if do_print_xml:
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61 print(XML.get('tests_start'))
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62
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63 for dataset in DATASETS:
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64 infile = os.path.join(test_dir, dataset+IN_EXT)
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65 outfile = os.path.join(test_dir, dataset+OUT_EXT)
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66
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67 if not os.path.exists(infile):
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68 sys.stderr.write("Error: file not found: "+infile+"\n")
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69 continue
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70 if not os.path.exists(outfile):
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71 sys.stderr.write("Error: file not found: "+outfile+"\n")
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72 continue
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73
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74 options = read_options(infile)
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75 if do_print_xml:
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76 print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
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77 else:
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78 run_tests(infile, outfile, options, script_dir)
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79
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80 if do_print_xml:
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81 print(XML.get('tests_end'))
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83
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84 def run_tests(infile, outfile, options, script_dir):
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85 script_cmd = os.path.join(script_dir, SCRIPT_NAME)+' '+options+' -i '+infile
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86 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
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87 print(script_cmd)
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88 subprocess.call(['bash', '-c', bash_cmd])
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90
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91 def print_xml(infile, outfile, options_str, xml, params, param_arg):
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92 infile = os.path.basename(infile)
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93 outfile = os.path.basename(outfile)
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94
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95 options = options_str.split() # on whitespace
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96
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97 print(xml.get('test_start'))
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98 print(xml.get('input') % infile)
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99
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100 # read in options one at a time, print <param> line
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101 i = 0
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102 while i < len(options):
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103 opt = options[i]
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104 if opt not in params or opt not in param_arg:
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105 sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "+infile+"\n")
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106 sys.exit(1)
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107 # takes argument
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108 if param_arg[opt]:
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109 i+=1
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110 arg = options[i]
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111 print(xml.get('param') % (params[opt], arg))
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112 # no argument (boolean)
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113 else:
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114 print(xml.get('param') % (params[opt], 'true'))
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115 i+=1
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116
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117 print(xml.get('output') % outfile)
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118 print(xml.get('test_end'))
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119
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120
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121 def read_options(infile):
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122 with open(infile, 'r') as infilehandle:
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123 for line in infilehandle:
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124 line.strip()
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125 if ARGS_KEY == line[:len(ARGS_KEY)]:
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126 return line[len(ARGS_KEY):-2]
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127 return ''
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128
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129
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130 if __name__ == '__main__':
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131 main()