def setUp(self):
self.options = Args()
self.options.config_file = get_file('defaults.cfg')
self.config = parse_config(self.options)
self.options.output_prefix = 'CEU'
self.options.chromosome = '5'
self.options.vcf_input = 'testcase.vcf'
self.template = CommandTemplate(self.options,self.config)
class TestRunPipeline(unittest.TestCase):
def setUp(self):
self.options = Args()
self.options.config_file = get_file('defaults.cfg')
self.config = parse_config(self.options)
self.options.output_prefix = 'CEU'
self.options.chromosome = '5'
self.options.vcf_input = 'testcase.vcf'
self.template = CommandTemplate(self.options,self.config)
def test_run_impute2(self):
(cmd_template, prefix) = self.template.run_impute2('test.haps')
assert prefix == \
self.options.output_prefix + self.options.chromosome +\
'_impute2'
assert cmd_template[0] == '/home/smilefreak/selectionTools/bin/impute2'
assert len(cmd_template) == 10
def test_remove_indels_vcf(self):
(cmd,output_name) = self.template.run_remove_indels_from_vcf()
assert output_name == 'testcase.recode.vcf'
assert len(cmd) == 7
assert cmd[0] == '/home/smilefreak/selectionTools/bin/vcftools'