IOError when input is empty. Rates and Errors set to 0 when no sites …

…are covered.

Sex.DetERRmine.py

@@ -3,7 +3,7 @@
 from math import sqrt
 from collections import OrderedDict
 
-VERSION="1.1.1"
+VERSION="1.1.2"
 
 def CalcErrors(AutSnps, XSnps, YSnps, NrAut, NrX, NrY):
     SNPs=[AutSnps, XSnps, YSnps]
@@ -15,16 +15,21 @@ def CalcErrors(AutSnps, XSnps, YSnps, NrAut, NrX, NrY):
     rate={}
     rateErr={}
 
-    for Bin,Idx in zip(["Aut", "X", "Y"], range(3)):
-        Total=sum(Reads)
-        p[Bin]=Reads[Idx]/Total
-        ErrNr[Bin]=sqrt(Total*p[Bin])
-        dp[Bin]=Reads[Idx]/SNPs[Idx]
-        Errdp[Bin]=ErrNr[Bin]/SNPs[Idx]
+    Total=sum(Reads)
 
-    for Bin in ["X","Y"]:
-        rate[Bin]=dp[Bin]/dp["Aut"]
-        rateErr[Bin]=sqrt((Errdp[Bin]/dp["Aut"])**2 + (Errdp["Aut"]*dp[Bin]/(dp["Aut"]**2))**2)
+    ## If no sites are covered at all, set error and rate to 0. 
+    if Total == 0:
+        (rate, rateErr) = ({"Aut":0.0,"X":0.0,"Y":0.0}, {"Aut":0.0,"X":0.0,"Y":0.0})
+    else :
+        for Bin,Idx in zip(["Aut", "X", "Y"], range(3)):
+            p[Bin]=Reads[Idx]/Total
+            ErrNr[Bin]=sqrt(Total*p[Bin])
+            dp[Bin]=Reads[Idx]/SNPs[Idx]
+            Errdp[Bin]=ErrNr[Bin]/SNPs[Idx]
+
+        for Bin in ["X","Y"]:
+            rate[Bin]=dp[Bin]/dp["Aut"]
+            rateErr[Bin]=sqrt((Errdp[Bin]/dp["Aut"])**2 + (Errdp["Aut"]*dp[Bin]/(dp["Aut"]**2))**2)
 
     return (rate, rateErr)
 
@@ -91,6 +96,12 @@ def CalcErrors(AutSnps, XSnps, YSnps, NrAut, NrX, NrY):
         if Chrom == "X":
             NrX[Names[x]]+=depths[Names[x]]
 
+if sum([AutSnps, XSnps, YSnps]) == 0:
+    raise IOError("""
+Input depth file is empty. Stopping execution.
+
+Please ensure you are using a bed file compatible with your reference genome coordinates.""")
+
 # SortNames=OrderedDict(sorted(Names.items(), key=lambda t: t[1]))
 print ("#Sample", "#SnpsAut", "#SNPsX", "#SnpsY", "NrAut", "NrX", "NrY", "x-rate", "y-rate", "Err(x-rate)", "Err(y-rate)", sep="\t", file=sys.stdout)
 data=OrderedDict()