Fix lint issues

Merge branch 'Regev32-MLO' into MLO

Author: pbashyal-nmdp

RunGrim.py

@@ -0,0 +1,77 @@
+import json
+import os
+import pandas as pd
+
+from graph_generation.generate_hpf import produce_hpf
+from grim.grim import graph_freqs
+from grim.grim import impute
+from filter_top_3 import change_donor_file
+from filter_by_rest import change_output_by_extra_gl
+
+
+def remove_empty_rows(file_path):
+    df = pd.read_csv(file_path)
+
+    df_cleaned = df.dropna(how="all")
+
+    df_cleaned.to_csv(file_path, index=False)
+
+
+def run_original_grim(
+    path_configuration, hap_pop_pair=True, Producehpf=False, dominant3=True
+):
+    with open(path_configuration, "r") as f:
+        config = json.load(f)
+
+    # first step in py-graph-imputation
+    if Producehpf:
+        produce_hpf(conf_file=path_configuration)
+
+        path_hpf = config["freq_file"]
+        # remove empty rows from hpf otherwise doesnt work
+        remove_empty_rows(path_hpf)
+
+        # second step in py-graph-imputation
+        graph_freqs(conf_file=path_configuration)
+
+    # changing donor file to 3 most imporatnt gls and returning short_gl,extra_gl for each row in donor
+    if dominant3:
+        path_donor = config["imputation_in_file"]
+
+        gls, lines = change_donor_file(path_donor)  # change so wont change donor file
+
+    # imputation
+    impute(conf_file=path_configuration, hap_pop_pair=hap_pop_pair)
+
+    # change the output and filter by the extra_gl
+    if dominant3:
+        path_pmug = os.path.join(
+            config["imputation_out_path"], config["imputation_out_hap_freq_filename"]
+        )
+        path_umug = os.path.join(
+            config["imputation_out_path"], config["imputation_out_umug_freq_filename"]
+        )
+        path_umug_pops = os.path.join(
+            config["imputation_out_path"], config["imputation_out_umug_pops_filename"]
+        )
+        path_pmug_pops = os.path.join(
+            config["imputation_out_path"], config["imputation_out_hap_pops_filename"]
+        )
+        path_miss = os.path.join(
+            config["imputation_out_path"], config["imputation_out_miss_filename"]
+        )
+
+        change_output_by_extra_gl(
+            config, gls, path_pmug, path_umug, path_umug_pops, path_pmug_pops, path_miss
+        )  # filter reasults in our origianl file, add miss to existing miss
+
+        # changing to original donor file
+        with open(path_donor, "w") as file:
+            for line in lines:
+                file.write(line)
+        file.close()
+
+
+if __name__ == "__main__":
+    conf_file = "conf/minimal-configuration.json"
+    run_original_grim(conf_file, True, True, True)

conf/minimal-configuration.json

@@ -2,7 +2,7 @@
   "populations": [
     "CAU"
   ],
-  "freq_trim_threshold": 1e-5,
+  "freq_trim_threshold": 0.1,
  "priority": {
    "alpha": 0.4999999,
     "eta": 0,
@@ -29,10 +29,10 @@
                 [[1], [2, 3], [4], [5]],
                 [[1], [2], [3], [4], [5]]
             ],
-  "planb": true,
+  "planb": false,
   "number_of_options_threshold": 100000,
   "epsilon": 1e-3,
-  "number_of_results": 10,
+  "number_of_results": 1000,
   "number_of_pop_results": 100,
   "output_MUUG": true,
   "output_haplotypes": true,