Source code for vcfparser.vcf_writer

[docs]class VCFWriter:
    """
    A vcf writer to write headerline and datalines into new file

    """

    def __init__(self, filename):
        self.w_file = open(filename, "a")


[docs]    def add_normal_metadata(self, key, value):
        """
        This is used to add normal key value metadata like: fileformat, filedate, refrence
        """
        print(f"##{key}= {value}\n", file=self.w_file)



[docs]    def add_info(self, id, num=".", type=".", desc="", key="INFO"):
        print(
            f'##{key}=<ID={id},Number={num},Type={type},Description="{desc}">\n',
            file=self.w_file,
        )



[docs]    def add_format(self, id, num=".", type=".", desc="", key="FORMAT"):
        print(
            f'##{key}=<ID={id},Number={num},Type={type},Description="{desc}">\n',
            file=self.w_file,
        )



[docs]    def add_filter(self, id, desc="", key="FILTER"):
        print(f'##{key}=<ID={id},Description="{desc}">\n', file=self.w_file)



[docs]    def add_filter_long(self, id, num=".", type=".", desc="", key="FILTER"):
        print(
            f'##{key}=<ID={id},Number={num},Type={type},Description="{desc}">\n',
            file=self.w_file,
        )



[docs]    def add_contig(self, id, length, key="contig"):
        # Example contig: ##contig=<ID=scaffold_591,length=5806>
        print(f"##{key}=<ID={id}, length={length}>\n", file=self.w_file)



[docs]    def add_header_line(self, record_keys):
        print(f"{record_keys}", sep="\t", file=self.w_file)



[docs]    def add_record_value(self, preheader, info, format_, sample_str):
        print(f"{preheader}", sep="\t", end="\t", file=self.w_file)
        print(f"{info}", sep="\t", end="\t", file=self.w_file)
        print(f"{format_}", sep="\t", end="\t", file=self.w_file)
        print(f"{sample_str}", sep="\t", end="\t", file=self.w_file)