Updating error messages and metafounder rules

Pedigree.py

@@ -95,7 +95,7 @@ def __init__(self, idx, idn, MetaFounder=None) :
 
         self.genotypedFounderStatus = None #?
 
-        self.MetaFounder = MetaFounder
+        self.MetaFounder = [MetaFounder] if MetaFounder is not None else None
 
         self.phenotype = None
 
@@ -536,7 +536,7 @@ def readInPedigreeFromList(self, pedList):
 
             # check if the individual is a metafounder
             if idx is not None and idx[:3] == "MF_":
-                print(f"ERROR: Invalid metafounder input format.\nExiting...")
+                print(f"ERROR: Individual {idx} uses the prefix 'MF_' which is reserved for metafounders and cannot be used for an individual's id. \nExiting...")
                 sys.exit(2)
 
             # All individuals (and dummy individuals) in the pedigree are assigned the default metafounder.
@@ -574,14 +574,11 @@ def readInPedigreeFromList(self, pedList):
                         # check if the metafounders match
                         if sireID == damID:
                             # Overwrite the default metafounder.
-                            ind.MetaFounder = sireID
+                            ind.MetaFounder = [sireID]
                         else:
-                            # expect more infomative error message
-                            print(f"ERROR: Invalid metafounder input format.\nExiting...")
-                            sys.exit(2)
+                            ind.MetaFounder = [sireID, damID]
                     else:
-                        # expect more infomative error message
-                        print(f"ERROR: Invalid metafounder input format.\nExiting...")
+                        print(f"ERROR: Both parents must be metafounders if one is a metafounder. For individual {idx} the parents were {sireID} and {damID}.\nConsider using a dummy individual for the metafounder.\nExiting...")
                         sys.exit(2)
                 else:
                     if sireID is None:
@@ -1010,7 +1007,7 @@ def readInAAP(self, fileName):
             mfx, data = value
             nLoci = self.nLoci
             if len(data) != nLoci:
-                print("ERROR: Incorrect alternative allele probability input format. \nExiting...")
+                print(f"ERROR: For {mfx}, not all loci have an alternative allele frequency in the `-alt_allele_prob_file` input. \nExiting...")
                 sys.exit(2)
             if mfx[:3] == "MF_":
                 if mfx == MainMetaFounder:
@@ -1019,11 +1016,11 @@ def readInAAP(self, fileName):
                 try:
                     current_aap[:] = data
                 except ValueError:
-                    print("ERROR: Incorrect alternative allele probability input format. \nExiting...")
+                    print(f"ERROR: For {mfx}, the alternative allele frequency data gave a ValueError. Please check the `-alt_allele_prob_file` input. \nExiting...")
                     sys.exit(2)
                 self.AAP[mfx] = current_aap
             else:
-                print("ERROR: Incorrect alternative allele probability input format. \nExiting...")
+                print(f"ERROR: All metafounders must have the prefix 'MF_'. {mfx} does not but is present in the `-alt_allele_prob_file`. Please remove or rename {mfx}. \nExiting...")
                 sys.exit(2)
 
         if default_aap:

ProbMath.py

@@ -13,6 +13,21 @@ def getGenotypesFromMaf(maf) :
 
     return mafGenotypes
 
+def getGenotypesFromMultiMaf(mafDict) :
+    nLoci = len(mafDict[list(mafDict.keys())[0]])
+    mafGenotypes = np.full((4, nLoci), .25, dtype = np.float32)
+    # Assumes two maf inputs.
+    # maf1 from the sire, maf2 from the dam.
+    maf1 = mafDict[list(mafDict.keys())[0]]
+    maf2 = mafDict[list(mafDict.keys())[1]]
+
+    mafGenotypes[0,:] = (1-maf1)*(1-maf2)
+    mafGenotypes[1,:] = (1-maf1)*(maf2)
+    mafGenotypes[2,:] = (maf1)*(1-maf2)
+    mafGenotypes[3,:] = maf1*maf2
+
+    return mafGenotypes
+
 def getGenotypeProbabilities_ind(ind, args = None, log = False):
     if args is None:
         error = 0.01