moved variantSeparation class to fun.py

LindoNkambule · Dec 2, 2019 · ffa7a6d · ffa7a6d
1 parent d25048e
commit ffa7a6d
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Showing 2 changed files with 55 additions and 54 deletions.
diff --git a/src/python/VCFCompare.py b/src/python/VCFCompare.py
@@ -2,59 +2,7 @@
 import os
 import argparse
 import csv
-from fun import infoExtract, createLists, concordance
-
-
-class variantSeparation:
-    def __init__(self, truth, query):
-        self.truth = truth
-        self.query = query
-
-
-    def SNVs(self):
-        snv = []
-        # Truth and Query
-        tsnv = createLists(self.truth).snvList()
-        truthSNVs = len(tsnv)
-        qsnv = createLists(self.query).snvList()
-        querySNVs = len(qsnv)
-
-        # Calls, Recall, and Precision
-        stp, sfp, sfn = concordance(tsnv, qsnv).variantCalls()
-        lenstp = len(stp)
-        lensfp = len(sfp)
-        lensfn = len(sfn)
-
-        try:
-            snvRecall = lenstp/(lenstp+lensfn)
-            snvPrecision = lenstp/(lenstp+lensfp)
-            snv.extend(('SNV', truthSNVs, lenstp, lensfp, lensfn, querySNVs, snvRecall, snvPrecision))
-        except Exception:
-            pass
-        return snv
-
-
-    def INDELs(self):
-        indel = []
-        # Truth and Query
-        tindel = createLists(self.truth).indelList()
-        truthINDELs = len(tindel)
-        qindel = createLists(self.query).indelList()
-        queryINDELs = len(qindel)
-
-        # Calls, Recall, and Precision
-        itp, ifp, ifn = concordance(tindel, qindel).variantCalls()
-        lenitp = len(itp)
-        lenifp = len(ifp)
-        lenifn = len(ifn)
-
-        try:
-            indelRecall = lenitp/(lenitp+lenifn)
-            indelPrecision = lenitp/(lenitp+lenifp)
-            indel.extend(('INDEL', truthINDELs, lenitp, lenifn, lenifn, queryINDELs, indelRecall, indelPrecision))
-        except Exception:
-            pass
-        return indel
+from fun import infoExtract, createLists, concordance, variantSeparation
 
 
 def main():
@@ -77,7 +25,7 @@ def main():
 
     truth_list = infoExtract(args.truth).alleles()
     query_list = infoExtract(args.query).alleles()
-    
+
 
     # Totals
     Truth_Total = len(truth_list)

diff --git a/src/python/fun.py b/src/python/fun.py
@@ -50,6 +50,59 @@ def snvINDELlists(self):
                 snvList.append(variant)
         return snvList, indelList
 
+
+class variantSeparation:
+    def __init__(self, truth, query):
+        self.truth = truth
+        self.query = query
+
+
+    def SNVs(self):
+        snv = []
+        # Truth and Query
+        tsnv = createLists(self.truth).snvList()
+        truthSNVs = len(tsnv)
+        qsnv = createLists(self.query).snvList()
+        querySNVs = len(qsnv)
+
+        # Calls, Recall, and Precision
+        stp, sfp, sfn = concordance(tsnv, qsnv).variantCalls()
+        lenstp = len(stp)
+        lensfp = len(sfp)
+        lensfn = len(sfn)
+
+        try:
+            snvRecall = lenstp/(lenstp+lensfn)
+            snvPrecision = lenstp/(lenstp+lensfp)
+            snv.extend(('SNV', truthSNVs, lenstp, lensfp, lensfn, querySNVs, snvRecall, snvPrecision))
+        except Exception:
+            pass
+        return snv
+
+
+    def INDELs(self):
+        indel = []
+        # Truth and Query
+        tindel = createLists(self.truth).indelList()
+        truthINDELs = len(tindel)
+        qindel = createLists(self.query).indelList()
+        queryINDELs = len(qindel)
+
+        # Calls, Recall, and Precision
+        itp, ifp, ifn = concordance(tindel, qindel).variantCalls()
+        lenitp = len(itp)
+        lenifp = len(ifp)
+        lenifn = len(ifn)
+
+        try:
+            indelRecall = lenitp/(lenitp+lenifn)
+            indelPrecision = lenitp/(lenitp+lenifp)
+            indel.extend(('INDEL', truthINDELs, lenitp, lenifn, lenifn, queryINDELs, indelRecall, indelPrecision))
+        except Exception:
+            pass
+        return indel
+
+
 class concordance():
     def __init__(self, truth, query):
         self.truth = truth