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_sate() # 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