added functions

LindoNkambule · Oct 24, 2019 · 4bdb528 · 4bdb528
1 parent 692d54a
commit 4bdb528
Showing 1 changed file with 27 additions and 0 deletions.
diff --git a/src/python/fun.py b/src/python/fun.py
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+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
+
+def snvINDELlists(snvList, indelList, variantsList):
+    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)
+    #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):
+    TPs = [x for x in query if x in truth]
+    FPs = [x for x in query if x not in truth]
+    FNs = [x for x in truth if x not in query]
+    return TPs, FPs, FNs