def test_samtools_wrapper(self): print "\n***** Testing Samtools_wrapper command *****\n" new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name) self.samtools_sort_test = wr_samtools.SamTools(self.wrapper_name, "test_samp", *self.add_args, **dict(new_base_kwargs)) print self.samtools_sort_test.run_command print self.samtools_sort_test.job_parms
def setUp(self): self.parmsfile = "test_wrappers_pe.yaml" self.rw1 = rsw(self.parmsfile) self.rw1.set_base_kwargs() self.rw1.parse_prog_info() self.wrapper_name = 'samtools_index' self.add_args = self.rw1.progs[self.wrapper_name] # use *self.add_args to unroll the list self.rw1.update_job_parms(self.wrapper_name) new_base_kwargs = self.rw1.update_prog_suffixes(self.wrapper_name) self.samtools_index_test = wr_samtools.SamTools( self.wrapper_name + "_round_2", "test_samp", *self.add_args, **dict(new_base_kwargs))