edited VariantUtils

dcicutils/variant_utils.py

@@ -1,14 +1,12 @@
 import json
-from dcicutils.ff_utils import get_metadata, get_health_page, search_metadata
+from dcicutils.ff_utils import get_metadata, search_metadata
 from dcicutils.creds_utils import CGAPKeyManager
 
-
-
 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_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='
 
     def __init__(self, *, env_name) -> None:
         self._key_manager = CGAPKeyManager()
@@ -19,81 +17,70 @@ def __init__(self, *, env_name) -> None:
 
     def get_creds(self):
         return self.creds
-
-    # Uncomment this if needed
-    # def get_health(self):
-    #     return self.health
-
-    def get_rare_variants_by_gene(self, *, gene, sort, addon = ''):
+
+    def get_rare_variants_by_gene(self, *, gene, sort, addon=''):
         """Does a search 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)
+        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"""
-        return len(set(variant.get('CALL_INFO') for variant in self.get_rare_variants_by_gene(gene=gene, sort='variant.ID')))
+        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"""
         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"""
-        sorted_list = sorted(unsorted_dict.items(), key=lambda x:x[1], reverse=True)
+        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"""
         mutation_dict = {}
-        unique_positions = set()   
+        unique_positions = set()
         for variant in self.get_rare_variants_by_gene(gene=gene, sort='variant.ID'):
-            pos = variant['variant']['POS']     
+            pos = variant['variant']['POS'] 
             if pos not in unique_positions:
                 unique_positions.add(pos)
                 mutation_dict[pos] = 1
             else:
                 mutation_dict[pos] += 1
         return {gene: self.sort_dict_in_descending_order({k: v for k, v in mutation_dict.items() if v >= 10})}
-    
+
     @staticmethod
     def return_json(file_name):
         with open(file_name, 'r') as f:
             file_content = json.loads(f)
         return file_content
-
 
     @staticmethod
     def create_dict_from_json_file(file_name):
         """creates dictionary object from json file"""
         with open(file_name) as f:
             json_list = f.read()
-        return json.loads(json_list) 
-
+        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')"""
         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 find_number_of_sample_ids(self, 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')))
-
+        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"""
         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 + '&variant.POS.from={pos}&variant.POS.to={pos}&sort=-DP'
-
+        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"""
         genes = self.return_json('gene.json')
-        return [gene['gene_symbol'] for gene in genes 
-                if 'Parkinson' in gene.get('gene_summary', '') 
-                or 'ALS' in gene.get('gene_summary', '')]
+        return [gene['gene_symbol'] for gene in genes
+                if 'Parkinson' in gene.get('gene_summary', '')
+                or 'ALS' in gene.get('gene_summary', '')]