def __init__(self, parent): # Save parent # self.composition, self.parent = parent, parent # Paths # self.p = AutoPaths(self.parent.p.stats_dir, self.all_paths) # Children # self.nmds = NMDS(self, self.parent.taxa_csv)
def __init__(self, parent): # Save parent # self.tax, self.parent = parent, parent # Paths # self.p = AutoPaths(self.parent.p.stats_dir, self.all_paths) # R stuff # self.nmds = NMDS(self, self.parent.otu_csv) self.permanova = PERMANOVA(self) self.betadis = BetaDispersion(self) # Other # self.unifrac = Unifrac(self)
def __init__(self, parent): # Save parent # self.stat, self.parent = parent, parent self.tax = parent.tax # Paths # self.p = AutoPaths(self.parent.p.unifrac_dir, self.all_paths) # Files # self.clustalo_aligned = FASTA(self.p.clustalo_align) self.pynast_aligned = FASTA(self.p.pynast_align) self.mothur_aligned = FASTA(self.p.mothur_align) self.raxml_tree = FilePath(self.p.raxml_tree) self.fasttree_tree = FilePath(self.p.fasttree_tree) self.distances_csv = CSVTable(self.p.distances_csv) # Graphs # self.nmds = NMDS(self, self.distances_csv, calc_distance=False)