cstrittmatter@0: """Ontology finder and visualizer"""
cstrittmatter@0: 
cstrittmatter@0: import copy, json, logging, requests, time
cstrittmatter@0: import pygraphviz as pgv
cstrittmatter@0: 
cstrittmatter@0: logging.getLogger('urllib3').setLevel(logging.WARNING)
cstrittmatter@0: 
cstrittmatter@0: 
cstrittmatter@0: # TODO: figure out what to do with root Thing:Thing
cstrittmatter@0: class Ontology_accession:
cstrittmatter@0:     '''Base class for defining attributes and behavior of single ontology accesions;
cstrittmatter@0:        Assume format definition (whitespace and punctuation okay):ontology_id'''
cstrittmatter@0:     existing_ontologies = {}
cstrittmatter@0: 
cstrittmatter@0:     @staticmethod
cstrittmatter@0:     def make_instance(acc):
cstrittmatter@0:       '''Use instead of default __init__ to enforce one instance per ontology'''
cstrittmatter@0:       try:
cstrittmatter@0:           return(Ontology_accession.existing_ontologies[acc])
cstrittmatter@0:       except(KeyError):
cstrittmatter@0:           Ontology_accession.existing_ontologies[acc] = Ontology_accession(acc)
cstrittmatter@0:           return(Ontology_accession.existing_ontologies[acc])
cstrittmatter@0: 
cstrittmatter@0:     def __init__(self, acc):
cstrittmatter@0:         '''If ontology is not recognized, just use short form, ex THING'''
cstrittmatter@0:         def_split = acc.split(':')
cstrittmatter@0:         self.label = ':'.join(def_split[:-1])
cstrittmatter@0:         self.id = def_split[-1].replace('_',':')
cstrittmatter@0:         self.parents = 'not assigned yet'
cstrittmatter@0:         self.children = 'not assigned yet'
cstrittmatter@0:         self.ancestors = 'not assigned yet'
cstrittmatter@0:         self.descendants = 'not assigned yet'
cstrittmatter@0:         self.graph_nodes = 'not assigned yet'
cstrittmatter@0:         self.graph_fill = False
cstrittmatter@0:         self.ontology = def_split[1].split('_')[0]
cstrittmatter@0:         if self.label == '':
cstrittmatter@0:             self._get_label()
cstrittmatter@0: 
cstrittmatter@0:     def _api_results(self, input_list, return_list):
cstrittmatter@0:         '''Ignore obsolete terms, not currently checking for \'term_replaced_by\''''
cstrittmatter@0:         for x_term in input_list:
cstrittmatter@0:             if x_term['is_obsolete']:
cstrittmatter@0:                 continue
cstrittmatter@0:             new_term = x_term['label'] + ':' + x_term['short_form']
cstrittmatter@0:             return_list.append(Ontology_accession.make_instance(new_term))
cstrittmatter@0:         return(return_list)
cstrittmatter@0: 
cstrittmatter@0:     def _add_edges(self, family_member, family_list, edge_set, round_num):
cstrittmatter@0:         '''Add edges to graph'''
cstrittmatter@0:         if edge_set == []:
cstrittmatter@0:             return(edge_set)
cstrittmatter@0:         elif round_num > 0:
cstrittmatter@0:             for x in family_list:
cstrittmatter@0:                 x.get_family(family_member)
cstrittmatter@0:                 if family_member == 'parents': # TODO: how get x.family_member to collapse code
cstrittmatter@0:                     if x.parents == ['none found']:
cstrittmatter@0:                         continue
cstrittmatter@0:                     if len(x.parents) > 5:
cstrittmatter@0:                         time.sleep(0.05)
cstrittmatter@0:                     new_edges = [(y._graph_label(),x._graph_label()) for y in x.parents]
cstrittmatter@0:                     edge_set = edge_set + [z for z in new_edges if z not in edge_set]
cstrittmatter@0:                     edge_set = x._add_edges(family_member, x.parents, edge_set, round_num-1)
cstrittmatter@0:                 elif family_member == 'children':
cstrittmatter@0:                     if x.children == ['none found']:
cstrittmatter@0:                         continue
cstrittmatter@0:                     if len(x.children) > 5:
cstrittmatter@0:                         time.sleep(0.05)
cstrittmatter@0:                     new_edges = [(x._graph_label(),y._graph_label()) for y in x.children]
cstrittmatter@0:                     edge_set = edge_set + [z for z in new_edges if z not in edge_set]
cstrittmatter@0:                     edge_set = x._add_edges(family_member, x.children, edge_set, round_num-1)
cstrittmatter@0:         return(edge_set)
cstrittmatter@0: 
cstrittmatter@0:     def _draw_graph(self, o_file, node_color, edge_color):
cstrittmatter@0:         '''Draw and save the graph'''
cstrittmatter@0:         ontol_graph = pgv.AGraph(name='ontology_graph')
cstrittmatter@0:         ontol_graph.add_node(self._graph_label())
cstrittmatter@0:         for x in self.graph_nodes:
cstrittmatter@0:             ontol_graph.add_edge(x[0], x[1])
cstrittmatter@0:         ontol_graph.node_attr.update(shape='box',
cstrittmatter@0:                                      style='rounded,filled',
cstrittmatter@0:                                      fillcolor='lightgrey',
cstrittmatter@0:                                      color=node_color)
cstrittmatter@0:         ontol_graph.edge_attr.update(shape='normal',
cstrittmatter@0:                                      color=edge_color,
cstrittmatter@0:                                      dir='back')
cstrittmatter@0:         ontol_graph.get_node(self._graph_label()).attr.update(fillcolor='lightblue')
cstrittmatter@0:         # TODO: determine best algorithm: neato, fdp, nop, twopi; tried circo; not dot, sfdp
cstrittmatter@0:         ontol_graph.draw(o_file, prog='twopi')
cstrittmatter@0: 
cstrittmatter@0:     def _expand_edge(self, family_member, family_list, edge_set, old_set='', stop_terms=False):
cstrittmatter@0:         '''Add edges to graph'''
cstrittmatter@0:         while old_set != edge_set:
cstrittmatter@0:             old_set = copy.deepcopy(edge_set)
cstrittmatter@0:         for x in family_list:
cstrittmatter@0:             if x == 'none found':
cstrittmatter@0:                 break
cstrittmatter@0:             if type(stop_terms) == list:
cstrittmatter@0:                 if x in stop_terms:
cstrittmatter@0:                     break
cstrittmatter@0:             x.get_family(family_member)
cstrittmatter@0:             if family_member == 'parents': # TODO: how get x.family_member to collapse code
cstrittmatter@0:                 if x.parents == ['none found']:
cstrittmatter@0:                     continue
cstrittmatter@0:                 if len(x.parents) > 5:
cstrittmatter@0:                     time.sleep(0.05)
cstrittmatter@0:                 new_edges = [(y._graph_label(),x._graph_label()) for y in x.parents]
cstrittmatter@0:                 edge_set = edge_set + [z for z in new_edges if z not in edge_set]
cstrittmatter@0:                 edge_set = x._expand_edge(family_member,x.parents,edge_set,old_set,stop_terms)
cstrittmatter@0:             elif family_member == 'children':
cstrittmatter@0:                 if x.children == ['none found']:
cstrittmatter@0:                     continue
cstrittmatter@0:                 if len(x.children) > 5:
cstrittmatter@0:                     time.sleep(0.05)
cstrittmatter@0:                 new_edges = [(x._graph_label(),y._graph_label()) for y in x.children]
cstrittmatter@0:                 edge_set = edge_set + [z for z in new_edges if z not in edge_set]
cstrittmatter@0:                 edge_set = x._expand_edge(family_member,x.children,edge_set,old_set,stop_terms)
cstrittmatter@0:         return(edge_set)
cstrittmatter@0: 
cstrittmatter@0:     def _get_label(self):
cstrittmatter@0:         '''Retrieve definition is correct for an id; updates instance'''
cstrittmatter@0:         query_url = 'http://www.ebi.ac.uk/ols/api/terms?obo_id={}'.format(self.id)
cstrittmatter@0:         ols_resp = self._get_request(query_url)
cstrittmatter@0:         if ols_resp is None:
cstrittmatter@0:             logging.warning(f'Did not retrieve PURL for {self.id}')
cstrittmatter@0:             self.label = 'unk'
cstrittmatter@0:             return
cstrittmatter@0:         try:
cstrittmatter@0:             self.label = ols_resp.json()['_embedded']['terms'][0]['label']
cstrittmatter@0:         except(KeyError):
cstrittmatter@0:             logging.warning(f'Did not find label for {self.id} in OLS')
cstrittmatter@0:             self.label = 'unk'
cstrittmatter@0:         except json.decoder.JSONDecodeError as err:
cstrittmatter@0:             time.sleep(0.05)
cstrittmatter@0:             self._get_label()
cstrittmatter@0: 
cstrittmatter@0:     def _get_request(self, request_url, max_retries=5):
cstrittmatter@0:         '''Retrieve URL'''
cstrittmatter@0:         while max_retries > 0:
cstrittmatter@0:             try:
cstrittmatter@0:                 return(requests.get(request_url))
cstrittmatter@0:             except:
cstrittmatter@0:                 time.sleep(0.05)
cstrittmatter@0:             max_retries -= 1
cstrittmatter@0:         return(None)
cstrittmatter@0: 
cstrittmatter@0:     def _graph_label(self):
cstrittmatter@0:         '''Format a graph label'''
cstrittmatter@0:         return(self.id+'\\n'+self.label)
cstrittmatter@0: 
cstrittmatter@0:     def _next_page(self, url_link, return_list):
cstrittmatter@0:         '''Get next page of search results'''
cstrittmatter@0:         next_resp = self._get_request(url_link)
cstrittmatter@0:         if next_resp is None:
cstrittmatter@0:             logging.warning(f'Did not retrieve URL for {url_link} during API search')
cstrittmatter@0:             return(False, return_list)
cstrittmatter@0:         else:
cstrittmatter@0:             try:
cstrittmatter@0:                 next_link = next_resp.json()['_links']['next']['href']
cstrittmatter@0:             except(KeyError):
cstrittmatter@0:                 next_link = False
cstrittmatter@0:             return_list = self._api_results(next_resp.json()['_embedded']['terms'], return_list)
cstrittmatter@0:         return(next_link, return_list)
cstrittmatter@0: 
cstrittmatter@0:     def check_label(self):
cstrittmatter@0:         '''Check if given definition is correct for an id; returns Boolean or str `unk`'''
cstrittmatter@0:         self._get_label()
cstrittmatter@0:         if self.label != 'unk':
cstrittmatter@0:             return(ols_resp.json()['_embedded']['terms'][0]['label'] == self.label)
cstrittmatter@0:         else:
cstrittmatter@0:             return(self.label)
cstrittmatter@0: 
cstrittmatter@0:     def get_family(self, family_member):
cstrittmatter@0:         '''Returns list of parents, ancestors, children or descendants'''
cstrittmatter@0:         if family_member == 'parents' and self.parents != 'not assigned yet':
cstrittmatter@0:             return(self.parents)
cstrittmatter@0:         elif family_member == 'children' and self.children != 'not assigned yet': 
cstrittmatter@0:             return(self.children)
cstrittmatter@0:         elif family_member == 'ancestors' and self.ancestors != 'not assigned yet': 
cstrittmatter@0:             return(self.ancestors)
cstrittmatter@0:         elif family_member == 'descendants' and self.descendants != 'not assigned yet': 
cstrittmatter@0:             return(self.descendants)
cstrittmatter@0: 
cstrittmatter@0:         if self.id.split(':')[0].lower() == 'gaz':
cstrittmatter@0:             query_url = 'https://www.ebi.ac.uk/ols/api/ontologies/gaz/terms?iri='
cstrittmatter@0:             query_url += 'http://purl.obolibrary.org/obo/' + self.id.replace(':','_')
cstrittmatter@0:             ols_resp = self._get_request(query_url)
cstrittmatter@0:             qry_url = ols_resp.json()['_embedded']['terms'][0]['_links']\
cstrittmatter@0:                                      ['hierarchical'+family_member.title()]['href']
cstrittmatter@0:         else:
cstrittmatter@0:             query_url = 'http://www.ebi.ac.uk/ols/api/ontologies/{}/{}?id={}'
cstrittmatter@0:             qry_url = query_url.format(self.id.split(':')[0].lower(),family_member,self.id)
cstrittmatter@0: 
cstrittmatter@0:         ols_resp = self._get_request(qry_url)
cstrittmatter@0:         if ols_resp is None:
cstrittmatter@0:             logging.warning(f'Did not get URL for {url_link} during search for {family_member}')
cstrittmatter@0:             result_list = ['none found']
cstrittmatter@0:         elif ols_resp.status_code > 200:
cstrittmatter@0:             result_list = ['none found']
cstrittmatter@0:         elif ols_resp.json()['page']['totalElements'] > 0:
cstrittmatter@0:             result_list = self._api_results(ols_resp.json()['_embedded']['terms'], [])
cstrittmatter@0:             if ols_resp.json()['page']['totalPages'] > 1:
cstrittmatter@0:                 next_url = ols_resp.json()['_links']['next']['href']
cstrittmatter@0:                 while next_url:
cstrittmatter@0:                     next_url,result_list = self._next_page(next_url,result_list)
cstrittmatter@0:         else:
cstrittmatter@0:             result_list = ['none found']
cstrittmatter@0: 
cstrittmatter@0:         if family_member == 'parents':
cstrittmatter@0:             self.parents = list(set(result_list))
cstrittmatter@0:         elif family_member == 'children':
cstrittmatter@0:             self.children = list(set(result_list))
cstrittmatter@0:         elif family_member == 'ancestors':
cstrittmatter@0:             self.ancestors = list(set(result_list))
cstrittmatter@0:         elif family_member == 'descendants':
cstrittmatter@0:             self.descendants = list(set(result_list))
cstrittmatter@0:         return(result_list)
cstrittmatter@0: 
cstrittmatter@0:     def bin_term(self, bin_package):
cstrittmatter@0:         '''Categorize term into given bins as Ontology_package'''
cstrittmatter@0:         term_bins = []
cstrittmatter@0:         self.get_family('ancestors')
cstrittmatter@0:         if self.ancestors == ['none found']:
cstrittmatter@0:             ancestor_labels = [x.label + ':' + x.id.replace(':','_') for x in [self]]
cstrittmatter@0:         else:
cstrittmatter@0:             ancestor_labels = [x.label+':'+x.id.replace(':','_') for x in [self]+self.ancestors]
cstrittmatter@0:         return([x for x in ancestor_labels if x in bin_package.ontologies])
cstrittmatter@0: 
cstrittmatter@0:     def visualize_term(self, o_file, node_color='black', edge_color='black',
cstrittmatter@0:                        fill_out=False, stop_terms=False, draw_graph=True):
cstrittmatter@0:         '''Visualize one term'''
cstrittmatter@0:         if self.graph_nodes!='not assigned yet' and self.graph_fill==fill_out:
cstrittmatter@0:             if draw_graph:
cstrittmatter@0:                 self._draw_graph(o_file, node_color, edge_color)
cstrittmatter@0:         else:
cstrittmatter@0:             self.get_family('parents')
cstrittmatter@0:             self.get_family('children')
cstrittmatter@0:             edge_set1,edge_set2 = [],[]
cstrittmatter@0:             if self.parents != ['none found']:
cstrittmatter@0:                 edge_set1 = [(x._graph_label(),self._graph_label()) for x in self.parents]
cstrittmatter@0:             if self.children != ['none found']:
cstrittmatter@0:                 edge_set2 = [(self._graph_label(),x._graph_label()) for x in self.children]
cstrittmatter@0:             if type(fill_out) == int:
cstrittmatter@0:                 edge_set1 = self._add_edges('parents', self.parents, edge_set1, fill_out-1)
cstrittmatter@0:                 edge_set2 = self._add_edges('children', self.children, edge_set2, fill_out-1)
cstrittmatter@0:             elif fill_out==True:
cstrittmatter@0:                 edge_set1 = self._expand_edge('parents',self.parents,edge_set1,'',stop_terms)
cstrittmatter@0:                 edge_set2 = self._expand_edge('children',self.children,edge_set2,'',stop_terms)
cstrittmatter@0:             self.graph_nodes = list(set(edge_set1+edge_set2))
cstrittmatter@0:             if draw_graph:
cstrittmatter@0:                 self._draw_graph(o_file, node_color, edge_color)
cstrittmatter@0: 
cstrittmatter@0: 
cstrittmatter@0: class Ontology_package:
cstrittmatter@0:     '''Associate or package Ontology_accession objects together'''
cstrittmatter@0:     def __init__(self, package_label, ontol_list):
cstrittmatter@0:         self.label = package_label
cstrittmatter@0:         self.ontologies = ontol_list
cstrittmatter@0:         self.bins = []
cstrittmatter@0:         self.lcp = 'not assigned yet'
cstrittmatter@0:         self.hcc = 'not assigned yet'
cstrittmatter@0:         self._lcp_state = (True,[])
cstrittmatter@0:         self._hcc_state = (True,[])
cstrittmatter@0:         self._bin_state = []
cstrittmatter@0:         self.graph_nodes = 'not assigned yet'
cstrittmatter@0:         self.graph_state = False
cstrittmatter@0: 
cstrittmatter@0:     def _common_family(self,family_member,incl_terms,excl_terms):
cstrittmatter@0:         '''Find common family members'''
cstrittmatter@0:         family_candidates = {}
cstrittmatter@0:         for ontol_term in [x for x in self.ontologies if x.id not in excl_terms]:
cstrittmatter@0:             family_candidates[ontol_term] = ontol_term.get_family(family_member)
cstrittmatter@0:         common_members = self._common_list(family_candidates, incl_terms)
cstrittmatter@0:         while common_members == []:
cstrittmatter@0:             for ontol_term in [x for x in self.ontologies if x.id not in excl_terms]:
cstrittmatter@0:                 if len(self.ontologies) > 30:
cstrittmatter@0:                     time.sleep(0.05)
cstrittmatter@0:                 original_list = list(family_candidates[ontol_term])
cstrittmatter@0:                 for family_ontol in original_list:
cstrittmatter@0:                     if len(original_list) > 30:
cstrittmatter@0:                         time.sleep(0.05)
cstrittmatter@0:                     try:
cstrittmatter@0:                         family_candidates[ontol_term].extend(\
cstrittmatter@0:                                                       family_ontol.get_family(family_member))
cstrittmatter@0:                     except(AttributeError):
cstrittmatter@0:                         family_candidates[ontol_term].extend(['none found'])
cstrittmatter@0:         return(common_members)
cstrittmatter@0: 
cstrittmatter@0:     def _common_list(self, input_dic, incl_terms):
cstrittmatter@0:         '''Compare input dictionary keys and list'''
cstrittmatter@0:         term_lists = []
cstrittmatter@0:         for ontol_key in input_dic:
cstrittmatter@0:             append_list = [ontol_key]
cstrittmatter@0:             for ontol_val in input_dic[ontol_key]:
cstrittmatter@0:                 append_list.append(ontol_val)
cstrittmatter@0:             term_lists.append(append_list)
cstrittmatter@0:         common_set = set.intersection(*map(set, term_lists))
cstrittmatter@0:         if incl_terms:
cstrittmatter@0:           common_keys = []
cstrittmatter@0:           for ontol_acc in common_set:
cstrittmatter@0:               if ontol_acc in input_dic.keys():
cstrittmatter@0:                   common_keys.append(ontol_acc)
cstrittmatter@0:               if common_keys != []:
cstrittmatter@0:                   return(common_keys)
cstrittmatter@0:         return(list(common_set - set(input_dic.keys())))
cstrittmatter@0: 
cstrittmatter@0:     def _draw_graph(self, o_file, node_color, edge_color, show_lcp, show_hcc):
cstrittmatter@0:         '''Draw and save graph'''
cstrittmatter@0:         ontol_graph = pgv.AGraph(name='ontology_graph')
cstrittmatter@0:         for x in self.ontologies:
cstrittmatter@0:             ontol_graph.add_node(x._graph_label())
cstrittmatter@0:         for x in self.graph_nodes:
cstrittmatter@0:             ontol_graph.add_edge(x[0], x[1])
cstrittmatter@0:         ontol_graph.node_attr.update(shape='box', style='rounded,filled',
cstrittmatter@0:                                      fillcolor='lightgrey', color=node_color)
cstrittmatter@0:         ontol_graph.edge_attr.update(shape='normal', color=edge_color, dir='back')
cstrittmatter@0:         if show_lcp:
cstrittmatter@0:             for x in self.lcp:
cstrittmatter@0:                 ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='beige')
cstrittmatter@0:         if show_hcc:
cstrittmatter@0:             for x in self.hcc:
cstrittmatter@0:                 ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='beige')
cstrittmatter@0:         for x in self.ontologies:
cstrittmatter@0:             ontol_graph.get_node(x._graph_label()).attr.update(fillcolor='lightblue')
cstrittmatter@0:         ontol_graph.draw(o_file,prog='dot')
cstrittmatter@0: 
cstrittmatter@0:     def _list_hierarchy(self, input_list, input_position):
cstrittmatter@0:         '''Get lowest or highest terms'''
cstrittmatter@0:         if input_list == ['none found']:
cstrittmatter@0:             return(input_list)
cstrittmatter@0:         family_lists = {}
cstrittmatter@0:         for input_term in input_list:
cstrittmatter@0:             if len(input_list) > 30: time.sleep(0.05)
cstrittmatter@0:             if input_position == 'lowest':
cstrittmatter@0:                 if input_term == 'none found':
cstrittmatter@0:                     family_list = 'none found'
cstrittmatter@0:                 else:
cstrittmatter@0:                     family_list = input_term.get_family('ancestors')
cstrittmatter@0:             elif input_position == 'highest':
cstrittmatter@0:                 if input_term == 'none found':
cstrittmatter@0:                     family_list = 'none found'
cstrittmatter@0:                 else:
cstrittmatter@0:                     family_list = input_term.get_family('descendants')
cstrittmatter@0:             family_lists[input_term] = family_list
cstrittmatter@0:         while True:
cstrittmatter@0:             remove_terms = []
cstrittmatter@0:             for input_term in input_list:
cstrittmatter@0:                 if [True for f_l in family_lists if input_term in family_lists[f_l]] != []:
cstrittmatter@0:                     del family_lists[input_term]
cstrittmatter@0:                     remove_terms.append(input_term)
cstrittmatter@0:             if remove_terms != []:
cstrittmatter@0:                 for x_term in remove_terms:
cstrittmatter@0:                     input_list.remove(x_term)
cstrittmatter@0:             else:
cstrittmatter@0:                 break
cstrittmatter@0:         return(input_list)
cstrittmatter@0: 
cstrittmatter@0:     def _trim_tips(self):
cstrittmatter@0:         '''Remove descendants of self.ontologies and parents of self.lcp'''
cstrittmatter@0:         tip_nodes = [x._graph_label() for x in self.ontologies] +\
cstrittmatter@0:                     [x._graph_label() for x in self.lcp]
cstrittmatter@0:         old_nodes = []
cstrittmatter@0:         while old_nodes != self.graph_nodes:
cstrittmatter@0:             old_nodes = self.graph_nodes
cstrittmatter@0:             right_nodes = set()
cstrittmatter@0:             left_nodes = set()
cstrittmatter@0:             for x in self.graph_nodes:
cstrittmatter@0:                 left_nodes.add(x[0])
cstrittmatter@0:                 right_nodes.add(x[1])
cstrittmatter@0:             top_nodes = [x for x in left_nodes.difference(right_nodes) if x not in tip_nodes]
cstrittmatter@0:             bot_nodes = [x for x in right_nodes.difference(left_nodes) if x not in tip_nodes]
cstrittmatter@0:             self.graph_nodes = [x for x in self.graph_nodes if x[0] not in top_nodes]
cstrittmatter@0:             self.graph_nodes = [x for x in self.graph_nodes if x[1] not in bot_nodes]
cstrittmatter@0: 
cstrittmatter@0:     def get_lcp(self, incl_terms=True, excl_terms=[]): # TODO: missing excl_terms
cstrittmatter@0:         '''Find lowest common parent(s); can include input terms as lcp,
cstrittmatter@0:            exclude terms by obo id; saves results in lcp attribute'''
cstrittmatter@0:         if self._lcp_state == (incl_terms, excl_terms):
cstrittmatter@0:             if self.lcp != 'not assigned yet':
cstrittmatter@0:                 return
cstrittmatter@0:         common_members = self._common_family('parents',incl_terms, excl_terms)
cstrittmatter@0:         common_members = self._list_hierarchy(common_members, 'lowest')
cstrittmatter@0:         if common_members != []:
cstrittmatter@0:             self.lcp = common_members
cstrittmatter@0:             self._lcp_state = (incl_terms, excl_terms)
cstrittmatter@0: 
cstrittmatter@0:     def get_hcc(self, incl_terms=True, excl_terms=[]):
cstrittmatter@0:         '''Get highest common child(ren); can include input terms as hcc;
cstrittmatter@0:            exclude terms by obo id; saves results in hcc attribute'''
cstrittmatter@0:         if self._hcc_state == (incl_terms, excl_terms):
cstrittmatter@0:             if self.hcc != 'not assigned yet':
cstrittmatter@0:                 return
cstrittmatter@0:         common_members = self._common_family('children', incl_terms, excl_terms)
cstrittmatter@0:         common_members = self._list_hierarchy(common_members, 'highest')
cstrittmatter@0:         if common_members != []:
cstrittmatter@0:             self.hcc = common_members
cstrittmatter@0:             self._hcc_state = (incl_terms, excl_terms)
cstrittmatter@0: 
cstrittmatter@0:     def set_lcp(self, lcp_acc, incl_terms=True, excl_terms=[]):
cstrittmatter@0:         self.lcp = lcp_acc
cstrittmatter@0:         self._lcp_state = (incl_terms, excl_terms)
cstrittmatter@0: 
cstrittmatter@0:     def set_hcc(self, hcc_acc, incl_terms=True, excl_terms=[]):
cstrittmatter@0:         self.hcc = hcc_acc
cstrittmatter@0:         self._hcc_state = (incl_terms, excl_terms)
cstrittmatter@0: 
cstrittmatter@0:     def bin_terms(self, bin_package):
cstrittmatter@0:         '''Categorize terms by those in Ontology_package; saves results in bins attribute'''
cstrittmatter@0:         if self._bin_state == bin_package:
cstrittmatter@0:             return
cstrittmatter@0:         package_bins = []
cstrittmatter@0:         for x in self.ontologies:
cstrittmatter@0:             package_bins.extend(x.bin_term(bin_package))
cstrittmatter@0:         self.bins = list(set(package_bins))
cstrittmatter@0: 
cstrittmatter@0:     def visualize_terms(self, o_file, fill_out=False, show_lcp=False, show_hcc=False,
cstrittmatter@0:                                       node_color='black', edge_color='black',
cstrittmatter@0:                                       lcp_stop=False, hcc_stop=False, trim_nodes=False):
cstrittmatter@0:         '''Visualize terms'''
cstrittmatter@0:         if self.graph_nodes=='not assigned yet' or self.graph_fill!=fill_out:
cstrittmatter@0:             self.graph_nodes = []
cstrittmatter@0:         for x in self.ontologies:
cstrittmatter@0:             if lcp_stop and not hcc_stop:
cstrittmatter@0:                 if x in self.lcp:
cstrittmatter@0:                     continue
cstrittmatter@0:                 x.visualize_term(o_file, fill_out=fill_out,
cstrittmatter@0:                                  stop_terms=self.lcp, draw_graph=False)
cstrittmatter@0:             elif hcc_stop and not lcp_stop:
cstrittmatter@0:                 if x in self.hcc:
cstrittmatter@0:                     continue
cstrittmatter@0:                 x.visualize_term(o_file, fill_out=fill_out, 
cstrittmatter@0:                                  stop_terms=self.hcc, draw_graph=False)
cstrittmatter@0:             elif hcc_stop and lcp_stop:
cstrittmatter@0:                 if x in self.lcp+self.hcc:
cstrittmatter@0:                     continue
cstrittmatter@0:                 x.visualize_term(o_file, fill_out=fill_out,
cstrittmatter@0:                                  stop_terms=self.lcp+self.hcc, draw_graph=False)
cstrittmatter@0:             else:
cstrittmatter@0:                 x.visualize_term(o_file, fill_out=fill_out, draw_graph=False)
cstrittmatter@0:             self.graph_nodes.extend([z for z in x.graph_nodes if z not in self.graph_nodes])
cstrittmatter@0:         if trim_nodes:
cstrittmatter@0:             self._trim_tips()
cstrittmatter@0:         if len(self.graph_nodes) > 150:
cstrittmatter@0:             edge_string = 'Parent node\tChild node'
cstrittmatter@0:             for edge_tuple in self.graph_nodes:
cstrittmatter@0:                 edge_string += '\n'+'\t'.join(edge_tuple)
cstrittmatter@0:             logging.info(f'Not drawing graph with {len(self.graph_nodes)} edges:\
cstrittmatter@0:                            \n\n{edge_string}\n')
cstrittmatter@0:         else:
cstrittmatter@0:             self._draw_graph(o_file,node_color,edge_color,show_lcp,show_hcc)