class PastaTeam (object):
'''A blob for holding the appropriate merger, alignment, and tree_estimator tools
as well as the TempFS object that keeps track of the directories that have
been created by this process.
'''
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.subsetalignmentjobs=[] #needed for interuptable job
self.subsets = {} # needed for pastamerger
self.alignmentjobs = [] # needed for pastamerger
self.interruptible=False
self.config = config
except AttributeError:
raise
raise ValueError("config cannot be None unless all of the tools are passed in.")
def get_temp_fs(self):
return self._temp_fs
temp_fs = property(get_temp_fs)
def change_aligner_to_custom(self):
self.aligner=self.config.create_aligner(temp_fs=self._temp_fs,custom=True)
def make_picklable(self):
self._temp_fs.make_picklable()
self.hmmeralign.make_picklable()
def make_unpickled(self):
self._temp_fs.make_unpickled()
self.hmmeralign.make_unpickled()
