Mercurial > repos > nick > allele_counts

comparison tests/run-tests.py @ 8:411adeff1eec draft

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Handle "." sample columns, update tests to work with BIAS column.
author nick
date Tue, 23 Aug 2016 02:30:56 -0400
parents 31361191d2d2
children 6cc488e11544
comparison
equal deleted inserted replaced
7:a72277535a2c 8:411adeff1eec
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 import os 2 import os
3 import sys 3 import sys
4 import subprocess 4 import subprocess
5 5
6 SCRIPT_NAME = 'allele-counts.py'
6 DATASETS = [ 7 DATASETS = [
7 'artificial', 8 'artificial',
8 'artificial-samples', 9 'artificial-samples',
9 'artificial-nofilt', 10 'artificial-nofilt',
10 'real', 11 'real',
14 ] 15 ]
15 IN_EXT = '.vcf.in' 16 IN_EXT = '.vcf.in'
16 OUT_EXT = '.csv.out' 17 OUT_EXT = '.csv.out'
17 ARGS_KEY = '##comment="ARGS=' 18 ARGS_KEY = '##comment="ARGS='
18 19
20 XML = {
21 'tests_start':' <tests>',
22 'test_start': ' <test>',
23 'input': ' <param name="input" value="tests/%s" />',
24 'param': ' <param name="%s" value="%s" />',
25 'output': ' <output name="output" file="tests/%s" />',
26 'test_end': ' </test>',
27 'tests_end': ' </tests>',
28 }
29 PARAMS = {
30 '-f':'freq',
31 '-c':'covg',
32 '-H':'header',
33 '-s':'stranded',
34 '-n':'nofilt',
35 '-r':'seed',
36 }
37 PARAM_ARG = {
38 '-f':True,
39 '-c':True,
40 '-H':False,
41 '-s':False,
42 '-n':False,
43 '-r':True,
44 }
45
19 def main(): 46 def main():
20 47
21 test_dir = os.path.dirname(os.path.relpath(sys.argv[0])) 48 do_print_xml = False
22 if test_dir: 49 if len(sys.argv) > 1:
23 test_dir += os.sep 50 if sys.argv[1] == '-x':
51 do_print_xml = True
52 else:
53 sys.stderr.write("Error: unrecognized option '"+sys.argv[1]+"'\n")
54 sys.exit(1)
55
56 test_dir = os.path.dirname(os.path.realpath(__file__))
57 script_dir = os.path.relpath(os.path.dirname(test_dir))
58 test_dir = os.path.relpath(test_dir)
59
60 if do_print_xml:
61 print XML.get('tests_start')
24 62
25 for dataset in DATASETS: 63 for dataset in DATASETS:
26 infile = test_dir+dataset+IN_EXT 64 infile = os.path.join(test_dir, dataset+IN_EXT)
27 outfile = test_dir+dataset+OUT_EXT 65 outfile = os.path.join(test_dir, dataset+OUT_EXT)
28 66
29 if not os.path.exists(infile): 67 if not os.path.exists(infile):
30 sys.stderr.write("Error: file not found: "+infile+"\n") 68 sys.stderr.write("Error: file not found: "+infile+"\n")
31 continue 69 continue
32 if not os.path.exists(outfile): 70 if not os.path.exists(outfile):
33 sys.stderr.write("Error: file not found: "+outfile+"\n") 71 sys.stderr.write("Error: file not found: "+outfile+"\n")
34 continue 72 continue
35 73
36 options = read_options(infile) 74 options = read_options(infile)
37 script_cmd = 'allele-counts.py '+options+' -i '+infile 75 if do_print_xml:
38 bash_cmd = 'diff '+outfile+' <('+script_cmd+')' 76 print_xml(infile, outfile, options, XML, PARAMS, PARAM_ARG)
39 # print infile+":" 77 else:
40 print script_cmd 78 run_tests(infile, outfile, options, script_dir)
41 subprocess.call(['bash', '-c', bash_cmd]) 79
80 if do_print_xml:
81 print XML.get('tests_end')
82
83
84 def run_tests(infile, outfile, options, script_dir):
85 script_cmd = os.path.join(script_dir, SCRIPT_NAME)+' '+options+' -i '+infile
86 bash_cmd = 'diff '+outfile+' <('+script_cmd+')'
87 print script_cmd
88 subprocess.call(['bash', '-c', bash_cmd])
89
90
91 def print_xml(infile, outfile, options_str, xml, params, param_arg):
92 infile = os.path.basename(infile)
93 outfile = os.path.basename(outfile)
94
95 options = options_str.split() # on whitespace
96
97 print xml.get('test_start')
98 print xml.get('input') % infile
99
100 # read in options one at a time, print <param> line
101 i = 0
102 while i < len(options):
103 opt = options[i]
104 if not params.has_key(opt) or not param_arg.has_key(opt):
105 sys.stderr.write("Error: unknown option '"+opt+"' in ARGS list in file "
106 +infile+"\n")
107 sys.exit(1)
108 # takes argument
109 if param_arg[opt]:
110 i+=1
111 arg = options[i]
112 print xml.get('param') % (params[opt], arg)
113 # no argument (boolean)
114 else:
115 print xml.get('param') % (params[opt], 'true')
116 i+=1
117
118 print xml.get('output') % outfile
119 print xml.get('test_end')
42 120
43 121
44 def read_options(infile): 122 def read_options(infile):
45 with open(infile, 'r') as infilehandle: 123 with open(infile, 'r') as infilehandle:
46 for line in infilehandle: 124 for line in infilehandle: