Avoid deeply nested control flow statements.

Open

                    for event in event0:
                        if 'los' in event:
                            los_parts = event.split(': ')
                            los_node = los_parts[1].replace('*','')
                            los_list.append(los_node)

Avoid deeply nested control flow statements.

Open

                    for hgt in hgt_list:
                        raw_hgt = hgt.split('-')
                        for hgt_part in raw_hgt:
                            if hgt_part in raw_los_list:
                                raw_los_list.remove(hgt_part)

Function subtreeMap has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

    def subtreeMap(self,species_node):

    # do the children of the current species node possess the
    # relevant genes?  if so, follow that child.  if not, return
    # the current node

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Avoid deeply nested control flow statements.

Open

                    if sscore < node_link.max_float:
                        # since python is insane, i can't directly
                        # remove things from this list.  instead, i'll
                        # just add them to a new list
                        orig_los_count = 0

Function GetPaths has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def GetPaths(root_node,this_node,root_lca,this_lca,path_dict,output_f):

Avoid deeply nested control flow statements.

Open

                        if found is True:
                            was_found = found
                            found_dist = new_dist

Avoid deeply nested control flow statements.

Open

                    if num_dups < 1 and num_loss < 1:
                        event0.extend(["[spc]: " + str(lcas_lca.species)])
                    # solicit input from event guide
                    if event_guide is not None:

Avoid deeply nested control flow statements.

Open

                    if node_link.best_score > sscore:
                        res['newick'] = MakeNewick(res,node_link,frac)
                        node_link.best_score = sscore
                        node_link.best_res = res

Avoid deeply nested control flow statements.

Open

                    if num_dups > 0:
                        dist_ratios.append('yes dup')
                    else:
                        dist_ratios.append('yes spc')

Avoid deeply nested control flow statements.

Open

                    for los in los_list:
                        raw_los_list.extend(los.split('-'))
                    for hgt in hgt_list:

Avoid deeply nested control flow statements.

Open

                    if event_guide is not None:
                        sscore -= EventGuideAdjust(event0,event_guide,model)

Function TryDL has 6 arguments (exceeds 4 allowed). Consider refactoring.

Open

def TryDL(parent1,parent2,node1,node2,node_link,lca_tables):

Avoid deeply nested control flow statements.

Open

                    if event_guide is not None:
                        print "can't do both HR and event guiding!"
                        sys.exit(1)

                    # are there any losses proposed?

Avoid deeply nested control flow statements.

Open

                    for los in hgt_list:
                        matched = False
                        for ind in range(len(los_list)):
                            this_los = "-" + los + "-"
                            if this_los in los_list[ind]:

Avoid deeply nested control flow statements.

Open

                    if sscore > node_link.best_score:
                        break
                else:

Avoid deeply nested control flow statements.

Open

                    for ind in range(len(los_list)):
                        los_list[ind] = "-" + los_list[ind] + "-"
                    los_list.sort(lambda a,b:len(a)-len(b))

Avoid deeply nested control flow statements.

Open

                    if parent is None:
                        upper_height = lower_height + 1.0
                    else:
                        upper_height = ultra_tree.height_dict[tree_link[parent]]
                    #endif

Function SaveResults has a Cognitive Complexity of 8 (exceeds 5 allowed). Consider refactoring.

Open

def SaveResults(output_args):
  ''' write the results of AnGSTs analysis to file '''

  model = output_args["model"]
  results_dirs = output_args["results"]

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Avoid deeply nested control flow statements.

Open

            if child_branch is not kid_branch:
                node.child_branches.append(child_branch)
                node.imposeHierarchy()

    # recursively label the roots of subtrees w/ the leaves contained

Function GetBranchDists has 5 arguments (exceeds 4 allowed). Consider refactoring.

Open

def GetBranchDists(this_node,this_lca,parent_lca,path_dict,output_f):