Mercurial > repos > nick > allele_counts_1

comparison tests/run-tests.py @ 12:97b772e3a0f1

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Uploaded tarball.
author nick
date Tue, 10 Sep 2013 13:14:07 -0400
parents 566e42c97532
children 44c3abd1b767
comparison
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11:566e42c97532 12:97b772e3a0f1
14 ] 14 ]
15 IN_EXT = '.vcf.in' 15 IN_EXT = '.vcf.in'
16 OUT_EXT = '.csv.out' 16 OUT_EXT = '.csv.out'
17 ARGS_KEY = '##comment="ARGS=' 17 ARGS_KEY = '##comment="ARGS='
18 18
19 XML = {
20 'tests_start':' <tests>',
21 'test_start': ' <test>',
22 'input': ' <param name="input" value="tests/%s" />',
23 'param': ' <param name="%s" value="%s" />',
24 'output': ' <output name="output" file="tests/%s" />',
25 'test_end': ' </test>',
26 'tests_end': ' </tests>',
27 }
28 PARAMS = {
29 '-f':'freq',
30 '-c':'covg',
31 '-H':'header',
32 '-s':'stranded',
33 '-n':'nofilt',
34 '-r':'seed',
35 }
36 PARAM_ARG = {
37 '-f':True,
38 '-c':True,
39 '-H':False,
40 '-s':False,
41 '-n':False,
42 '-r':True,
43 }
44
45 def main(): 19 def main():
46
47 do_print_xml = False
48 if len(sys.argv) > 1:
49 if sys.argv[1] == '-x':
50 do_print_xml = True
51 else:
52 sys.stderr.write("Error: unrecognized option '"+sys.argv[1]+"'\n")
53 sys.exit(1)
54 20
55 test_dir = os.path.dirname(os.path.relpath(sys.argv[0])) 21 test_dir = os.path.dirname(os.path.relpath(sys.argv[0]))
56 if test_dir: 22 if test_dir:
57 test_dir += os.sep 23 test_dir += os.sep
58
59 if do_print_xml:
60 print XML.get('tests_start')
61 24
62 for dataset in DATASETS: 25 for dataset in DATASETS:
63 infile = test_dir+dataset+IN_EXT 26 infile = test_dir+dataset+IN_EXT
64 outfile = test_dir+dataset+OUT_EXT 27 outfile = test_dir+dataset+OUT_EXT
65 28
69 if not os.path.exists(outfile): 32 if not os.path.exists(outfile):
70 sys.stderr.write("Error: file not found: "+outfile+"\n") 33 sys.stderr.write("Error: file not found: "+outfile+"\n")
71 continue 34 continue
72 35
73 options = read_options(infile) 36 options = read_options(infile)
74 if do_print_xml: 37 script_cmd = 'allele-counts.py '+options+' -i '+infile
75 print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG) 38 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
76 else: 39 # print infile+":"
77 run_tests(infile, outfile, options) 40 print script_cmd
78 41 subprocess.call(['bash', '-c', bash_cmd])
79 if do_print_xml:
80 print XML.get('tests_end')
81
82
83 def run_tests(infile, outfile, options):
84 script_cmd = 'allele-counts.py '+options+' -i '+infile
85 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
86 print script_cmd
87 subprocess.call(['bash', '-c', bash_cmd])
88
89
90 def print_xml(infile, outfile, options_str, xml, params, param_arg):
91 infile = os.path.basename(infile)
92 outfile = os.path.basename(outfile)
93
94 options = options_str.split() # on whitespace
95
96 print xml.get('test_start')
97 print xml.get('input') % infile
98
99 i = 0
100 while i < len(options):
101 opt = options[i]
102 if not params.has_key(opt) or not param_arg.has_key(opt):
103 sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "
104 +infile+"\n")
105 sys.exit(1)
106 if param_arg[opt]:
107 i+=1
108 arg = options[i]
109 print xml.get('param') % (params[opt], arg)
110 else:
111 print xml.get('param') % (params[opt], opt)
112 i+=1
113
114 print xml.get('output') % outfile
115 print xml.get('test_end')
116 42
117 43
118 def read_options(infile): 44 def read_options(infile):
119 with open(infile, 'r') as infilehandle: 45 with open(infile, 'r') as infilehandle:
120 for line in infilehandle: 46 for line in infilehandle: