def __init__(self): AbstractAlgorithm.__init__(self) self.place_nomatch_fragments = False ''' Hardcoded E-Lim for hmmsearch ''' #TODO: what to do with this self.elim = 99999999 self.filters = False self.strategy = options().exhaustive.strategy self.minsubsetsize = int(options().exhaustive.minsubsetsize) #Temp fix for now, self.molecule = self.options.molecule
def read_alignment_and_tree(self): (alignment, tree) = AbstractAlgorithm.read_alignment_and_tree(self) # TODO: Check for rooted input # if not tree.is_rooted: # raise Exception ("For TIPP, backbone tree should be correctly # rooted according to the taxonomy.") return (alignment, tree)
def check_options(self, supply=[]): if (options().info_file is None): supply = supply + ["raxml file"] AbstractAlgorithm.check_options(self, supply)
def check_options(self, supply = []): AbstractAlgorithm.check_options(self,supply)