def set_up(self): self.ts = TempFS() self.ts.create_top_level_temp(prefix='runSateTest', parent=TESTS_DIR) self.job_name = 'satejob' + self.random_id(8) self.dirs = set([self.ts.top_level_temp]) self.paths = set()
def __init__(self, config): """Uses a configuration object `cfg` to get reference for the tools the user has chosen. """ try: max_mem_mb = config.sate.max_mem_mb self._temp_fs = TempFS() self.aligner = config.create_aligner(temp_fs=self._temp_fs) self.aligner.max_mem_mb = max_mem_mb self.hmmeralign = config.create_aligner(temp_fs=self._temp_fs, name="hmmeralign") self.merger = config.create_merger(temp_fs=self._temp_fs) self.merger.max_mem_mb = max_mem_mb self.tree_estimator = config.create_tree_estimator( temp_fs=self._temp_fs) self.raxml_tree_estimator = config.create_tree_estimator( name='Raxml', temp_fs=self._temp_fs) self.subsets = {} # needed for pastamerger self.alignmentjobs = [] # needed for pastamerger self.treeshrink_wrapper = config.create_treeshrink_wrapper( temp_fs=self._temp_fs) except AttributeError: raise raise ValueError( "config cannot be None unless all of the tools are passed in.")
def setUp(self): self.ts = TempFS() self.ts.create_top_level_temp(prefix='treeEstimatorTest', parent=os.curdir) self.filename = data_source_path('mafft.anolis.fasta') self.alignment = Alignment() self.alignment.read_filepath(data_source_path('mafft.anolis.fasta'), 'FASTA')
def setUp(self): self.ts = TempFS()
def setUp(self): self.ts = TempFS() self.ts.create_top_level_temp(prefix='alignerTesting', parent=os.curdir)