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)
class StatsOnTaxonomy(object):
"""All the statistics to perform on an OTU table that has taxonomy
associated to it."""
all_paths = """
/nmds/
/permanova/
/betadis/
/unifrac/
"""
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 run(self):
self.nmds.run()
self.permanova.run()
self.betadis.run()
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)
class StatsOnComposition(object):
all_paths = """
/nmds/
/permanova/
/betadis/
"""
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 run(self):
self.nmds.run()
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)