fixed ZerroDivisionError for VCFs without SNVs or INDELs

LindoNkambule · Nov 5, 2019 · 39fe23e · 39fe23e
1 parent 518aee1
commit 39fe23e
Show file tree

Hide file tree

Showing 2 changed files with 18 additions and 12 deletions.
diff --git a/TODO.md b/TODO.md
@@ -1,9 +1,10 @@
 Todo list for VCFCompare
 ====
 
-##Tasks
+## Tasks
 
-- [ ] 1. Add png output for upset plots. The current output format is PDF
-- [ ] 2. Currently, the program assumes both the truth and query VCF files contain both SNVs and INDELs. If one (or both, SNVs and INDELs) are not present in the of two files, you will get a ZeroDivisionError
-- [ ] 3. Write a function for handling no-ALT alleles
-- [ ] 4. Write a function for genotype concordance
+- [ ] 1. Parallelize the comparison for SNVs and INDELs to save time
+- [ ] 2. Add png output for upset plots. The current output format is PDF
+- [x] 3. Currently, the program assumes both the truth and query VCF files contain both SNVs and INDELs. If one or both (SNVs and INDELs) are not present in the two files, you will get a ZeroDivisionError
+- [ ] 4. Write a function for handling no-ALT alleles
+- [ ] 5. Write a function for genotype concordance
diff --git a/src/python/VCFCompare.py b/src/python/VCFCompare.py
@@ -58,20 +58,25 @@ def main():
     lensfp = len(sfp)
     lensfn = len(sfn)
 
-    snvRecall = lenstp/(lenstp+lensfn)
-    snvPrecision = lenstp/(lenstp+lensfp)
+    try:
+        snvRecall = lenstp/(lenstp+lensfn)
+        snvPrecision = lenstp/(lenstp+lensfp)
+        snv.extend(('SNV', truthSNVs, lenstp, lensfp, lensfn, querySNVs, snvRecall, snvPrecision))
+    except Exception:
+        print("No SNVs were detected in one or both the files")
 
     #2.INDELs
     itp, ifp, ifn = fun.variantCalls(tindel, qindel)
     lenitp = len(itp)
     lenifp = len(ifp)
     lenifn = len(ifn)
 
-    indelRecall = lenitp/(lenitp+lenifn)
-    indelPrecision = lenitp/(lenitp+lenifp)
-
-    snv.extend(('SNV', truthSNVs, lenstp, lensfp, lensfn, querySNVs, snvRecall, snvPrecision))
-    indel.extend(('INDEL', truthINDELs, lenitp, lenifn, lenifn, queryINDELs, indelRecall, indelPrecision))
+    try:
+        indelRecall = lenitp/(lenitp+lenifn)
+        indelPrecision = lenitp/(lenitp+lenifp)
+        indel.extend(('INDEL', truthINDELs, lenitp, lenifn, lenifn, queryINDELs, indelRecall, indelPrecision))
+    except Exception:
+        print("No INDELs were detected in one or both the files")
 
     csvfile = args.output + ".csv"
     with open(csvfile, "w", newline='') as f: