From 2e9baa9290402cb0e6d76d944ecc0871c2e8be54 Mon Sep 17 00:00:00 2001
From: LindoNkambule <lindonkambule116@gmail.com>
Date: Sat, 30 Nov 2019 20:45:11 +0200
Subject: [PATCH] grouped functions into methods under classes

---
 src/python/fun.py | 116 +++++++++++++++++++++++++---------------------
 1 file changed, 63 insertions(+), 53 deletions(-)

diff --git a/src/python/fun.py b/src/python/fun.py
index d156487..34185fa 100644
--- a/src/python/fun.py
+++ b/src/python/fun.py
@@ -1,55 +1,65 @@
 #!/usr/bin/env python
 
-def vcfExtract(vcf):
-    import allel
-    vcfInfo = allel.vcf_to_dataframe(vcf, ['variants/CHROM', 'variants/POS', 'variants/REF', 'variants/ALT'], alt_number=1)
-    return vcfInfo
-    #extract information from vcf to a df
-
-def vcfDFtoList(vcfdf):
-    vcfList = vcfdf.values.tolist()
-    return vcfList
-    #convert df to a list
-
-#for SNVs only
-def snvList(variantsList):
-    snvList = []
-    for variant in variantsList:
-        ref = len(str(variant[2]))
-        alt = len(str(variant[3]))
-        if(ref == 1 and alt == 1):
-            snvList.append(variant)
-    return snvList
-
-#for INDELs only
-def indelList(variantsList):
-    indelList = []
-    for variant in variantsList:
-        ref = len(str(variant[2]))
-        alt = len(str(variant[3]))
-        if (ref > 1 or alt > 1):
-            indelList.append(variant)
-    return indelList
-
-#for both SNVs and INDELs
-def snvINDELlists(variantsList):
-    snvList = []
-    indelList = []
-    for variant in variantsList:
-        ref = len(str(variant[2]))
-        alt = len(str(variant[3]))
-        if (ref > 1 or alt > 1):
-            indelList.append(variant)
-        else:
-            snvList.append(variant)
-    return snvList, indelList
-    #separate SNVs and INDELs into separate lists
-    #this function takes (1) two empty SNV and INDEL lists and (2) a list with variants, and separates the variants according to size (SNVs and INDELs)
-
-def variantCalls(truth, query):
-    Truth_set = set(map(tuple, truth)) #convert nested lists to sets for speed
-    Query_Set = set(map(tuple, query))
-    TPs = Truth_set.intersection(Query_Set)
-    FPs = Query_Set.difference(Truth_set)
-    FNs = Truth_set.difference(Query_Set)
-    return TPs, FPs, FNs
+
+class infoExtract:
+    def __init__(self, vcf):
+        self.vcf = vcf
+
+
+    def alleles(self):
+        import allel
+        vcfInfo = allel.vcf_to_dataframe(self.vcf, ['variants/CHROM', 'variants/POS', 'variants/REF', 'variants/ALT'], alt_number=1)
+        vcfList = vcfInfo.values.tolist()
+        return vcfList
+
+
+class createLists():
+    def __init__(self, variantsList):
+        self.variantsList = variantsList
+
+
+    def snvList(self):
+        snvList = []
+        for variant in self.variantsList:
+            ref = len(str(variant[2]))
+            alt = len(str(variant[3]))
+            if(ref == 1 and alt == 1):
+                snvList.append(variant)
+        return snvList
+
+
+    def indelList(self):
+        indelList = []
+        for variant in self.variantsList:
+            ref = len(str(variant[2]))
+            alt = len(str(variant[3]))
+            if (ref > 1 or alt > 1):
+                indelList.append(variant)
+        return indelList
+
+
+    def snvINDELlists(self):
+        snvList = []
+        indelList = []
+        for variant in self.variantsList:
+            ref = len(str(variant[2]))
+            alt = len(str(variant[3]))
+            if (ref > 1 or alt > 1):
+                indelList.append(variant)
+            else:
+                snvList.append(variant)
+        return snvList, indelList
+
+class concordance():
+    def __init__(self, truth, query):
+        self.truth = truth
+        self.query = query
+
+
+    def variantCalls(self):
+        Truth_set = set(map(tuple, self.truth))
+        Query_Set = set(map(tuple, self.query))
+        TPs = Truth_set.intersection(Query_Set)
+        FPs = Query_Set.difference(Truth_set)
+        FNs = Truth_set.difference(Query_Set)
+        return TPs, FPs, FNs