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)
