VariantUtils edited

dcicutils/variant_utils.py

@@ -5,10 +5,11 @@
 
 class VariantUtils:
 
-    SEARCH_VARIANTS_BY_GENE = '/search/?type=VariantSample&limit=1&variant.genes.genes_most_severe_gene.display_title='
-    SEARCH_RARE_VARIANTS_BY_GENE = '/search/?samplegeno.samplegeno_role=proband&type=VariantSample\
-        &variant.csq_gnomadg_af_popmax.from=0&variant.csq_gnomadg_af_popmax.to=0.001\
-            &variant.genes.genes_most_severe_gene.display_title='
+    SEARCH_VARIANTS_BY_GENE = (f'/search/?type=VariantSample&limit=1'
+                               f'&variant.genes.genes_most_severe_gene.display_title=')
+    SEARCH_RARE_VARIANTS_BY_GENE = (f'/search/?samplegeno.samplegeno_role=proband&type=VariantSample'
+                                    f'&variant.csq_gnomadg_af_popmax.from=0&variant.csq_gnomadg_af_popmax.to=0.001'
+                                    f'&variant.genes.genes_most_severe_gene.display_title=')
 
     def __init__(self, *, env_name) -> None:
         self._key_manager = CGAPKeyManager()
@@ -21,28 +22,29 @@ def get_creds(self):
         return self.creds
 
     def get_rare_variants_by_gene(self, *, gene, sort, addon=''):
-        """Does a search for rare variants on a particular gene"""
+        """Searches for rare variants on a particular gene"""
         return search_metadata(f'{self.base_url}/{self.SEARCH_RARE_VARIANTS_BY_GENE}{gene}\
                                &sort=-{sort}{addon}', key=self.creds)
 
     def find_number_of_sample_ids(self, gene):
-        """returns the number of samples that have a mutation on the specified gene"""
+        """Returns the number of samples that have a mutation on the specified gene"""
         return len(set(variant.get('CALL_INFO')
                        for variant in self.get_rare_variants_by_gene(gene=gene, sort='variant.ID')))
 
     def get_total_result_count_from_search(self, gene):
-        """returns total number of variants associated with specified gene"""
+        """Returns total number of variants associated with specified gene"""
         res = get_metadata(self.SEARCH_VARIANTS_BY_GENE + gene, key=self.creds)
         return res['total']
 
     @staticmethod
     def sort_dict_in_descending_order(unsorted_dict):
-        """sorts dictionary in descending value order"""
+        """Sorts dictionary in descending value order"""
         sorted_list = sorted(unsorted_dict.items(), key=lambda x: x[1], reverse=True)
         return dict(sorted_list)
 
     def create_dict_of_mutations(self, gene):
-        """cretes dictionary of specified gene and 10+ occuring positions with their number of variants"""
+        """Creates dictionary of specified gene and mutations that occur 10+ times in database, in the form:
+            {gene: {mutation1 pos: #variants, mutation2 pos: #variants, ...}"""
         mutation_dict = {}
         unique_positions = set()
         for variant in self.get_rare_variants_by_gene(gene=gene, sort='variant.ID'):
@@ -62,26 +64,28 @@ def return_json(file_name):
 
     @staticmethod
     def create_dict_from_json_file(file_name):
-        """creates dictionary object from json file"""
+        """Creates dictionary object from specified json file"""
         with open(file_name) as f:
             json_list = f.read()
         return json.loads(json_list)
 
     def create_list_of_msa_genes(self):
-        """creates list of all genes relating to the brain or nervous system (by 'neur' and 'nerv')"""
+        """Creates list of genes relating to the brain or nervous system
+            (determined by whether keywords 'neur' or 'nerv' in summary)"""
         genes = self.return_json('gene.json')
         return [gene['gene_symbol'] for gene in genes
                 if 'nerv' in gene.get('gene_summary', '')
                 or 'neur' in gene.get('gene_summary', '')]
 
     def create_url(self, gene):
-        """returns a url to the variants at the most commonly mutated position of a gene"""
+        """Returns a url to the variants at the most commonly mutated position of specified gene"""
         d = self.create_dict_from_json_file('10+sorted_msa_genes_and_mutations.json')
         pos = list(d[gene].keys())[0]
         return self.SEARCH_RARE_VARIANTS_BY_GENE + gene + f'&variant.POS.from={pos}&variant.POS.to={pos}&sort=-DP'
 
     def create_list_of_als_park_genes(self):
-        """cretes list of genes that mention Parkinson's or ALS in their summary"""
+        """Creates list of genes that relating to Parkinson's or ALS
+            (determined by whether keywords 'Parkinson' or 'ALS' in summary)"""
         genes = self.return_json('gene.json')
         return [gene['gene_symbol'] for gene in genes
                 if 'Parkinson' in gene.get('gene_summary', '')