Merge branch 'develop' of github.com:alliance-genome/agr_genedescript…

…ions into develop
alliance-genome · Jan 2, 2020 · 3fbd06e · 3fbd06e
2 parents aba9480 + ab01677
commit 3fbd06e
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Showing 3 changed files with 12 additions and 9 deletions.
diff --git a/genedescriptions/ontology_tools.py b/genedescriptions/ontology_tools.py
@@ -104,6 +104,7 @@ def set_all_depths_in_subgraph(ontology: Ontology, root_id: str, relations: List
 
 
 def set_ic_ontology_struct(ontology: Ontology, relations: List[str] = None):
+    logger.info("Setting information content values based on ontology structure")
     roots = ontology.get_roots(relations=relations)
     for root_id in roots:
         if "num_subsumers" not in ontology.node(root_id) and ("type" not in ontology.node(root_id) or
@@ -121,6 +122,7 @@ def set_ic_ontology_struct(ontology: Ontology, relations: List[str] = None):
         if "type" not in ontology.node(root_id) or ontology.node_type(root_id) == "CLASS":
             _set_information_content_in_subgraph(ontology=ontology, root_id=root_id,
                                                  maxleaves=ontology.node(root_id)["num_leaves"], relations=relations)
+    logger.info("Finished setting information content values")
 
 
 def set_ic_annot_freq(ontology: Ontology, annotations: AssociationSet):

diff --git a/genedescriptions/stats.py b/genedescriptions/stats.py
@@ -38,11 +38,10 @@ def __init__(self):
     @staticmethod
     def _get_num_covered_nodes(set_initial_terms, set_final_terms, ontology):
         num_covered_nodes = 0
-        final_t_ancestors = {final_term: ontology.ancestors(final_term) for final_term in set_final_terms}
         for initial_term in set_initial_terms:
             initial_t_ancestors = set(ontology.ancestors(initial_term, reflexive=True))
             for final_term in set_final_terms:
-                if final_term in initial_t_ancestors or initial_term in final_t_ancestors[final_term]:
+                if final_term in initial_t_ancestors:
                     num_covered_nodes += 1
                     break
         return num_covered_nodes

diff --git a/tests/test_trimming.py b/tests/test_trimming.py
@@ -24,8 +24,8 @@ def setUp(self):
         self.df = DataManager(do_relations=None, go_relations=["subClassOf", "BFO:0000050"])
         logging.basicConfig(filename=None, level="ERROR", format='%(asctime)s - %(name)s - %(levelname)s: %(message)s')
         self.df.load_ontology_from_file(ontology_type=DataType.GO, ontology_url="file://" + os.path.join(
-            self.this_dir, "data", "go_gd_test.obo"),
-                                        ontology_cache_path=os.path.join(self.this_dir, "cache", "go_gd_test.obo"),
+            self.this_dir, "data", "go.obo"),
+                                        ontology_cache_path=os.path.join(self.this_dir, "cache", "go_test.obo"),
                                         config=self.conf_parser)
         logger.info("Loading go associations from file")
         self.df.load_associations_from_file(associations_type=DataType.GO, associations_url="file://" + os.path.join(
@@ -124,18 +124,20 @@ def test_trimming_lca(self):
 
         self.conf_parser.config["go_sentences_options"]["trimming_algorithm"] = "lca"
         self.conf_parser.config["expression_sentences_options"]["trimming_algorithm"] = "lca"
-        gene = Gene(id="SGD:S000007393", name="acr-5", dead=False, pseudo=False)
-        associations = self.get_associations(gene.id, ['GO:0003723', 'GO:0003887', 'GO:0003964', 'GO:0004540',
-                                                       'GO:0008233'], [""], "F", "ISS")
+        gene = Gene(id='HGNC:10301', name="RPL11", dead=False, pseudo=False)
+        associations = self.get_associations(gene.id, ['GO:1904667', 'GO:2000059', 'GO:0032092', 'GO:2000435',
+                                                       'GO:0010628', 'GO:0000027', 'GO:1901796', 'GO:0050821',
+                                                       'GO:0006364', 'GO:0002181', 'GO:0042273', 'GO:0006605'], [""],
+                                             "P", "EXP")
         self.df.go_associations = AssociationSetFactory().create_from_assocs(
             assocs=associations, ontology=self.df.go_ontology)
-        gene_desc_lca = GeneDescription(gene_id=gene.id, config=self.conf_parser, gene_name="YDR210W-B",
+        gene_desc_lca = GeneDescription(gene_id=gene.id, config=self.conf_parser, gene_name="RPL11",
                                         add_gene_name=False)
         set_gene_ontology_module(dm=self.df, conf_parser=self.conf_parser, gene_desc=gene_desc_lca, gene=gene)
         gene_desc_lca.stats.calculate_stats(data_manager=self.df)
         self.conf_parser.config["go_sentences_options"]["trimming_algorithm"] = "ic"
         self.conf_parser.config["expression_sentences_options"]["trimming_algorithm"] = "ic"
-        gene_desc_ic = GeneDescription(gene_id=gene.id, config=self.conf_parser, gene_name="YDR210W-B",
+        gene_desc_ic = GeneDescription(gene_id=gene.id, config=self.conf_parser, gene_name="RPL11",
                                        add_gene_name=False)
         set_gene_ontology_module(dm=self.df, conf_parser=self.conf_parser, gene_desc=gene_desc_ic, gene=gene)
         gene_desc_ic.stats.calculate_stats(data_manager=self.df)