def setUp(self):
self.set_up()
self.tmp_sub_dir = self.ts.create_temp_subdir(
parent=self.ts.top_level_temp, prefix='MultiLocusDatasetTest')
self.data_path = os.path.join(self.tmp_sub_dir,
self.job_name + '_test.fasta')
self.mlds = MultiLocusDataset()
def _impl_test_tree_estimator(self, name, datatype, partitions, **kwargs):
num_cpus = kwargs.get('num_cpus', None)
filename = data_source_path('anolis.fasta')
md = MultiLocusDataset()
md.read_files(seq_filename_list=[filename],
datatype=datatype)
md.relabel_for_pasta()
# alignment = Alignment()
# alignment.read_filepath(filename, 'FASTA')
te = self.get_tree_estimator(name)
if te is None:
_LOG.warn("test%s skipped" % name)
return
# alignment.datatype = datatype
if num_cpus:
a = te.run(alignment=md,
partitions=partitions,
tmp_dir_par=self.ts.top_level_temp,
delete_temps=True,
num_cpus=num_cpus)
else:
a = te.run(alignment=md,
partitions=partitions,
tmp_dir_par=self.ts.top_level_temp,
delete_temps=True)
def read_input_sequences(seq_filename_list,
datatype,
missing=None):
md = MultiLocusDataset()
md.read_files(seq_filename_list=seq_filename_list,
datatype=datatype,
missing=missing)
return md
