[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

geneplexus/_geneplexus.py

@@ -65,7 +65,13 @@ def _initial_id_convert(input_genes, file_loc, species):
                     converted_gene_name = ", ".join(all_to_name)
                     logger.debug(f"Found mapping ({anIDtype}) {agene} -> {all_convert_dict[anIDtype][agene]}")
                     break
-            convert_out.append([agene, converted_gene or "Could Not be mapped to Entrez" ,converted_gene_name or "Could Not be mapped to Entrez"])
+            convert_out.append(
+                [
+                    agene,
+                    converted_gene or "Could Not be mapped to Entrez",
+                    converted_gene_name or "Could Not be mapped to Entrez",
+                ]
+            )
 
     column_names = ["Original ID", "Entrez ID", "Gene Name"]
     df_convert_out = pd.DataFrame(convert_out, columns=column_names).astype(str)
@@ -100,7 +106,7 @@ def _get_genes_in_network(file_loc, species, net_type, convert_ids):
     return pos_genes_in_net, genes_not_in_net, net_genes
 
 
-def _get_negatives(file_loc, species, net_type, gsc, pos_genes_in_net,user_negatives):
+def _get_negatives(file_loc, species, net_type, gsc, pos_genes_in_net, user_negatives):
     gsc_full = util.load_gsc(file_loc, species, gsc, net_type)
     uni_genes = np.array(gsc_full["Universe"])
     gsc_terms = gsc_full["Term_Order"]
@@ -118,9 +124,11 @@ def _get_negatives(file_loc, species, net_type, gsc, pos_genes_in_net,user_negat
         pval = hypergeom.sf(k - 1, M, n, N)
         if pval < 0.05:
             genes_to_remove = np.union1d(genes_to_remove, n_set)
-            neutral_gene_info[akey] = {"Name": gsc_full[akey]["Name"],
-                                       "Task": gsc_full[akey]["Task"],
-                                       "Genes": n_set}
+            neutral_gene_info[akey] = {
+                "Name": gsc_full[akey]["Name"],
+                "Task": gsc_full[akey]["Task"],
+                "Genes": n_set,
+            }
     neutral_gene_info["All Neutrals"] = np.setdiff1d(genes_to_remove, pos_genes_in_net).tolist()
     negative_genes = np.setdiff1d(uni_genes, genes_to_remove)
     return negative_genes, neutral_gene_info
@@ -230,7 +238,7 @@ def _make_prob_df(file_loc, sp_trn, sp_tst, net_type, probs, pos_genes_in_net, n
 
 def _make_sim_dfs(file_loc, mdl_weights, species, gsc, net_type, features):
     # make task conversion
-    task_convert = {"Mondo":"Disease", "Monarch":"Phenotype", "GO":"Biological Process"}
+    task_convert = {"Mondo": "Disease", "Monarch": "Phenotype", "GO": "Biological Process"}
     weights_dict = util.load_pretrained_weights(file_loc, species, gsc, net_type, features)
     gsc_full = util.load_gsc(file_loc, species, gsc, net_type)
     gsc_terms = gsc_full["Term_Order"]

geneplexus/geneplexus.py

@@ -1,13 +1,13 @@
 """GenePlexus API."""
 import os
 import os.path as osp
-import numpy as np
 import warnings
 from typing import Any
 from typing import Dict
 from typing import List
 from typing import Optional
 
+import numpy as np
 import pystow
 import yaml
 
@@ -54,7 +54,7 @@ def __init__(
             input_genes: Input gene list, can be mixed type. Can also be set
                 later if not specified at init time by simply calling
                 :meth:`load_genes` (default: :obj:`None`).
-            input_negatives: Input list of negative genes, can be mixed type. 
+            input_negatives: Input list of negative genes, can be mixed type.
                 Can also be set later if not specified at init time by simply calling
                 :meth:`load_negatives` (default: :obj:`None`).
             auto_download: Automatically download necessary files if set.
@@ -96,7 +96,7 @@ def __init__(
 
         if input_genes is not None:
             self.load_genes(input_genes)
-            
+
         if input_negatives is not None:
             self.load_genes(load_negatives)
 
@@ -130,7 +130,7 @@ def _params(self) -> List[str]:
             "auto_download",
             "log_level",
             "input_genes",
-            "input_negatives"
+            "input_negatives",
         ]
 
     def dump_config(self, outdir: str):
@@ -254,7 +254,7 @@ def load_genes(self, input_genes: List[str]):
         self.table_summary = load_genes_outputs[1]
         self.selfinput_count = load_genes_outputs[2]
         self.convert_ids = load_genes_outputs[3]
-        
+
     def load_negatives(self, input_negatives: List[str]):
         """Load gene list and convert to Entrez that will used as negatives.
 
@@ -409,8 +409,8 @@ def _get_pos_and_neg_genes(self):
             self.convert_ids,
         )
         if len(self.input_negatives) > 0:
-            # remove genes from negatives if they are also positives 
-            user_negatives = np.setdiff1d(self.convert_ids_negatives,self.convert_ids).tolist()
+            # remove genes from negatives if they are also positives
+            user_negatives = np.setdiff1d(self.convert_ids_negatives, self.convert_ids).tolist()
             print(user_negatives)
         else:
             user_negatives = None
@@ -420,9 +420,9 @@ def _get_pos_and_neg_genes(self):
             self.net_type,
             self.gsc_trn,
             self.pos_genes_in_net,
-            user_negatives
+            user_negatives,
         )
-        
+
         return self.pos_genes_in_net, self.negative_genes, self.net_genes, self.neutral_gene_info
 
     def make_sim_dfs(self):

geneplexus/util.py

@@ -229,7 +229,8 @@ def load_gsc(
     """
     file_name = f"GSC__{species}__{gsc}__{net_type}.json"
     return _load_json_file(file_loc, file_name)
-
+
+
 def load_biomart(