def check_ingroup_clade_composition(self, ingrp_clade_node, species_dict):
ingrp_clade_leaves_arr = get_node_leaves(ingrp_clade_node)
ingrp_clade_species_dict = self.ingrp_clade_species_count(ingrp_clade_leaves_arr)
no_of_represented_species = self.compare_species_compositions(ingrp_clade_species_dict, species_dict)
if no_of_represented_species:
return 1
else:
return 0
def process_family_tree(self, fam_tree, outgrp_re, species_dict):
ingroup_clade_arr = list()
clade_counter = 1
clade_filename = BasePath.outpath + "/" + self.fam_id + "/" + self.fam_id + BasePath.clade_fileextension
clade_file = open(clade_filename, "w")
for node in fam_tree.traverse("levelorder"):
leaf_arr = get_node_leaves(node)
if check_for_outgroups(leaf_arr, outgrp_re):
flag = self.check_for_clade_overlap(leaf_arr, ingroup_clade_arr)
if flag == 1:
clade_flag = self.check_ingroup_clade_composition(node, species_dict)
if clade_flag == 1:
self.print_clade_sequences(node, self.fam_id, clade_counter, clade_file)
clade_counter += 1
clade_file.close()
def inspect_ingroup_pairs(self, fam_tree, ingroup_pair_arr, outgrp_re):
fp_pair_count = 0
tp_pair_count = 0
for ingroup_pair in ingroup_pair_arr:
pair_mrca = fam_tree.get_common_ancestor(ingroup_pair[0],
ingroup_pair[1])
pair_mrca_leaf_arr = get_node_leaves(pair_mrca)
outgrp_flag = check_for_outgroups(pair_mrca_leaf_arr, outgrp_re)
if outgrp_flag == 1:
tp_pair_count += 1
else:
fp_pair_count += 1
precision_val = self.calculate_precison_value(tp_pair_count,
fp_pair_count)
return precision_val
def get_regex_matching_sequence_list_from_node(fam_tree, regex):
leaf_arr = get_node_leaves(fam_tree)
sequence_matches_arr = list(filter(regex.search, leaf_arr))
return sequence_matches_arr
def get_ingroup_sequence_list(self, fam_tree, ingrp_re):
leaf_arr = get_node_leaves(fam_tree)
ingroup_matches_arr = self.get_ingroup_sequences(leaf_arr, ingrp_re)
return ingroup_matches_arr
def check_if_tree_contains_outgroups(fam_tree, outgrp_re):
leaf_arr = get_node_leaves(fam_tree)
flag = check_for_outgroups(leaf_arr, outgrp_re)
return flag
