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'