update for pip

Author: sapiris

grim/conf/minimal-configuration.json

@@ -11,6 +11,7 @@
     "gamma": 1e-7,
     "delta": 0.4999999
   },
+  "UNK_priors": "SR",
   "FULL_LOCI": "ABCQR",
    "loci_map": {
     "A": 1,
@@ -19,6 +20,7 @@
     "DQB1": 4,
     "DRB1": 5
   },
+
   "factor_missing_data": 0.0001,
   "Plan_B_Matrix": [
                 [[1, 2, 3, 4, 5]],

grim/imputation/imputegl/impute.py

@@ -110,6 +110,7 @@ def __init__(self, net=None,config=None,  count_by_prob=None, verbose=False):
             self.populations = config["pops"]
             self.netGraph = net
             self.priorMatrix = np.ones((len(self.populations), len(self.populations)))
+            self.unk_priors = config["UNK_priors"]
 
             # For plan b
             #self.full_loci = config["full_loci"]
@@ -1419,7 +1420,11 @@ def call_comp_phase_prob(self, epsilon, n, phases, chr, MUUG_output, planb):
         # no plan b
         for level in range(2):
             if level == 1:
-                self.priorMatrix = np.ones((len(self.populations), len(self.populations)))  ####
+                if self.unk_priors == "MR":
+                    self.priorMatrix = np.ones((len(self.populations), len(self.populations)))
+                else:
+                    self.priorMatrix = np.identity(len(self.populations))
+                #self.priorMatrix = np.ones((len(self.populations), len(self.populations)))  ####
             if planb and len(res['Haps']) == 0:
                 self.plan = 'b'
                 epsilon = 1e-14
@@ -1615,7 +1620,10 @@ def update_prob_by_priority(self, res, race1, race2, priority):
 
     def impute_one(self, subject_id, gl, binary, race1, race2, priority, epsilon, n, MUUG_output, haps_output, planb, em):#em
         clean_gl = clean_up_gl(gl)
-        self.priorMatrix =  np.ones((len(self.populations), len(self.populations)))
+        if self.unk_priors == "MR":
+            self.priorMatrix =  np.ones((len(self.populations), len(self.populations)))
+        else:
+            self.priorMatrix = np.identity(len(self.populations))
         to_calc_prior_matrix = False
         if race1 or race2:
             race1 = race1.split(';')

grim/validation/runfile.py

@@ -67,7 +67,8 @@ def run_impute(conf_file = "../conf/minimal-configuration.json", project_dir_gra
         "max_haplotypes_number_in_phase": json_conf.get("max_haplotypes_number_in_phase",100 ),
         "bin_imputation_input_file": project_dir_in_file + json_conf.get("bin_imputation_in_file", "None"),
         "nodes_for_plan_A": json_conf.get("Plan_A_Matrix", []),
-        "save_mode": json_conf.get("save_space_mode", False)
+        "save_mode": json_conf.get("save_space_mode", False),
+        "UNK_priors" : json_conf.get("UNK_priors", "MR")
 
     }
 
@@ -76,6 +77,7 @@ def run_impute(conf_file = "../conf/minimal-configuration.json", project_dir_gra
     print("Performing imputation based on:")
     print("\tPopulation: {}".format(config["pops"]))
     print("\tPriority: {}".format(config["priority"]))
+    print("\tPriority: {}".format(config["UNK_priors"]))
     print("\tEpsilon: {}".format(config["epsilon"]))
     print("\tPlan B: {}".format(config["planb"]))
     print("\tNumber of Results: {}".format(config["number_of_results"]))