Ruff lint, format, sort imports

genmod/annotate_models/__init__.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 
-from .make_haploblocks import get_haploblocks
+from .fix_variant import make_print_version
 from .genetic_models import check_genetic_models
+from .make_haploblocks import get_haploblocks
 from .model_score import get_model_score
-from .fix_variant import make_print_version
 from .variant_annotator import VariantAnnotator

genmod/annotate_models/fix_variant.py

@@ -1,90 +1,78 @@
 from . import get_model_score
 
+
 def make_print_version(variant, families):
     """
     Get the variants ready for printing
-    
+
     This function collects the annotations added and merge them in the INFO
     dict.
-    
+
     Arguments:
         variant (dict): A variant dictionary
-    
+
     """
-    
-    variant_id = variant['variant_id']
-    vcf_info = variant['INFO'].split(';')
-    
-    feature_list = variant.get('annotation', set())
-    
+
+    variant_id = variant["variant_id"]
+    vcf_info = variant["INFO"].split(";")
+
+    feature_list = variant.get("annotation", set())
+
     # variant[compounds] is a dictionary with family id as keys and a set of compounds as values
-    compounds = variant.get('compounds', dict())
+    compounds = variant.get("compounds", dict())
     # Here we store the compound strings that should be added to the variant:
     family_compound_strings = []
 
-    genetic_models = variant.get('inheritance_models', {})
+    genetic_models = variant.get("inheritance_models", {})
 
     # We need to check if compounds have already been annotated.
-    if 'Compounds' not in variant['info_dict']:
-
+    if "Compounds" not in variant["info_dict"]:
         for family_id in compounds:
-            if (genetic_models[family_id].get('AR_comp') or genetic_models[family_id].get('AR_comp_dn')):
-                compound_string = ''
+            if genetic_models[family_id].get("AR_comp") or genetic_models[family_id].get(
+                "AR_comp_dn"
+            ):
+                compound_string = ""
                 compound_set = compounds[family_id]
-                #We do not want reference to itself as a compound:
+                # We do not want reference to itself as a compound:
                 compound_set.discard(variant_id)
                 # If there are any compounds for the family:
                 if compounds[family_id]:
-                    compound_string = '|'.join(compound_set)
-                    family_compound_strings.append(':'.join([family_id, compound_string]))
-                
+                    compound_string = "|".join(compound_set)
+                    family_compound_strings.append(":".join([family_id, compound_string]))
+
                 if len(family_compound_strings) > 0:
-                    vcf_info.append('Compounds=' + ','.join(family_compound_strings))
-    
+                    vcf_info.append("Compounds=" + ",".join(family_compound_strings))
+
     # Check if any genetic models are followed
-    if 'GeneticModels' not in variant['info_dict']:
+    if "GeneticModels" not in variant["info_dict"]:
         # Here we store the compound strings that should be added to the variant:
         family_model_strings = []
         model_scores = {}
         for family_id in genetic_models:
-            model_string = ''
+            model_string = ""
             model_list = []
             for model in genetic_models[family_id]:
                 if genetic_models[family_id][model]:
                     model_list.append(model)
-                model_string = '|'.join(model_list)
+                model_string = "|".join(model_list)
             if len(model_list) > 0:
-                family_model_strings.append(':'.join(
-                                            [family_id, model_string]))
-
+                family_model_strings.append(":".join([family_id, model_string]))
+
                 model_scores[family_id] = str(
-                    get_model_score(families[family_id].individuals, variant))
-
+                    get_model_score(families[family_id].individuals, variant)
+                )
+
         if len(family_model_strings) > 0:
-            vcf_info.append(
-                        'GeneticModels={0}'.format( 
-                        ','.join(family_model_strings)))
+            vcf_info.append("GeneticModels={0}".format(",".join(family_model_strings)))
 
             model_score_list = []
             for family_id in model_scores:
                 if model_scores[family_id]:
                     if float(model_scores[family_id]) > 0:
-                        model_score_list.append(
-                            ':'.join(
-                                        [
-                                            family_id, 
-                                            model_scores[family_id]
-                                        ]
-                                    )
-                                )
+                        model_score_list.append(":".join([family_id, model_scores[family_id]]))
             if len(model_score_list) > 0:
-                vcf_info.append(
-                            'ModelScore=' +  
-                            ','.join(model_score_list)
-                            )
-
-
-
-    variant['INFO'] = ';'.join(vcf_info)
+                vcf_info.append("ModelScore=" + ",".join(model_score_list))
+
+    variant["INFO"] = ";".join(vcf_info)
 
     return variant