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))