VCF_tools.py

class VCF_CNV:

    def __init__(self):
        self.CHROM = 0
        self.POS = 0
        self.ID = "."
        self.REF = "."
        self.ALT = "."
        self.QUAL = 6
        self.FILTER = "PASS"
        self.SVTYPE = None
        self.END = 0
        self.SVLEN = 0
        self.CIPOS = "0,0"
        self.CIEND = "0,0"
        self.GENE = "."
        self.FORMAT = "GT:GQ"
        self.SAMPLE = ".:0"

    def __repr__(self):
        vcf = "{}\t{}\t{}\t{}\t{}\t{}\t{}\tSVTYPE={};END={};SVLEN={};CIPOS={};CIEND={};GENE={}\t{}\t{}".format(self.CHROM,self.POS,self.ID,self.REF,self.ALT,self.QUAL,self.FILTER,self.SVTYPE,self.END,self.SVLEN,self.CIPOS,self.CIEND,self.GENE,self.FORMAT,self.SAMPLE)
        return vcf