Refactor/issue 266 warnings

src/tinypeel/Peeling/PeelingIO.py

@@ -1,6 +1,7 @@
 import numpy as np
 from numba import jit
 from ..tinyhouse import InputOutput
+import warnings
 
 
 def readInSeg(pedigree, fileName, start=None, stop=None):
@@ -58,7 +59,9 @@ def readInSeg(pedigree, fileName, start=None, stop=None):
                 )
 
             if idx not in pedigree.individuals:
-                print(f"Individual {idx} is not found in pedigree. Individual ignored.")
+                warnings.warn(
+                    f"Individual {idx} is not found in pedigree. Individual ignored."
+                )
             else:
                 ind = pedigree.individuals[idx]
                 if e == 0:
@@ -74,7 +77,9 @@ def readInSeg(pedigree, fileName, start=None, stop=None):
                 indHit[ind.idn] += 1
         for ind in pedigree:
             if indHit[ind.idn] != 4:
-                print(f"No segregation information found for individual {ind.idx}")
+                warnings.warn(
+                    f"No segregation information found for individual {ind.idx}"
+                )
 
     return seg
 

src/tinypeel/Peeling/PeelingInfo.py

@@ -2,6 +2,7 @@
 from numba.experimental import jitclass
 import numpy as np
 from collections import OrderedDict
+import warnings
 
 from ..tinyhouse import ProbMath
 from ..tinyhouse import HaplotypeOperations
@@ -149,18 +150,18 @@ def createPeelingInfo(pedigree, args, createSeg=True, phaseFounder=False):
 
     if args.penetrance is not None:
         if peelingInfo.isXChr:
-            print(
+            warnings.warn(
                 "Using an external penetrance file and the x_chr option is highly discouraged. Please do not use."
             )
 
         if args.est_geno_error_prob:
-            print(
+            warnings.warn(
                 "External penetrance file included, but est_geno_error_prob flag used. The two options are incompatible. est_geno_error_prob set to false."
             )
             args.est_geno_error_prob = False
 
         if args.est_seq_error_prob:
-            print(
+            warnings.warn(
                 "External penetrance file included, but est_seq_error_prob flag used. The two options are incompatible. est_seq_error_prob set to false."
             )
             args.est_seq_error_prob = False
@@ -265,7 +266,9 @@ def addPenetranceFromExternalFile(pedigree, peelingInfo, fileName, args):
             penetranceLine = np.array([float(val) for val in parts], dtype=np.float32)
 
             if idx not in pedigree.individuals:
-                print("Individual", idx, "not found in pedigree. Individual ignored.")
+                warnings.warn(
+                    "Individual", idx, "not found in pedigree. Individual ignored."
+                )
             else:
                 ind = pedigree.individuals[idx]
                 peelingInfo.penetrance[ind.idn, e, :] *= penetranceLine

src/tinypeel/Peeling/PeelingUpdates.py

@@ -5,6 +5,8 @@
 
 from . import PeelingInfo
 
+import warnings
+
 #########################################################################################
 # In this module we will update 3 things:                                               #
 # 1) Our estimate for the MAF (both prior to peeling and after each peeling cycle) .    #
@@ -30,7 +32,7 @@ def updateMaf(pedigree, peelingInfo):
     :return: None. The function updates the pedigree.AAP attribute with the new alternative allele frequencies.
     """
     if peelingInfo.isXChr:
-        print(
+        warnings.warn(
             "Updating error rates and alternative allele frequencies for X chromosomes are not well test and will break in interesting ways. Recommend running without that option."
         )
     MF = list(pedigree.AAP.keys())
@@ -256,7 +258,7 @@ def updatePenetrance(pedigree, peelingInfo, args):
         peelingInfo.seqError = updateSeqError(pedigree, peelingInfo)
 
     if peelingInfo.isXChr:
-        print(
+        warnings.warn(
             "Updating error rates and minor allele frequencies for X chromosomes are not well test and will break in interesting ways. Recommend running without that option."
         )
     phaseFounder = not args.no_phase_founder

src/tinypeel/tinypeel.py

@@ -859,7 +859,7 @@ def main():
 
     singleLocusMode = args.method == "single"
     if args.method == "multi" and args.segfile:
-        print("Running in multi-locus mode, external segfile ignored")
+        warnings.warn("Running in multi-locus mode, external segfile ignored")
 
     # For now, only support a single phenotype (will remove in future)
     if args.phenotype is not None and pedigree.nPheno > 1: