Source code for bioconvert.bcf2vcf

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# Bioconvert is a project to facilitate the interconversion               #
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"""Convert :term:`BCF` file to :term:`VCF` format"""
import colorlog

from bioconvert import ConvBase
from bioconvert.core.decorators import requires

logger = colorlog.getLogger(__name__)


class BCF2VCF(ConvBase):
    """Convert :term:`BCF` file to :term:`VCF` file

    Methods available are based on bcftools [BCFTOOLS]_.

    """

    _default_method = "bcftools"

    def __init__(self, infile, outfile, *args, **kargs):
        """.. rubric:: constructor

        :param str infile: input BCF file
        :param str outfile: output VCF file

        """
        super(BCF2VCF, self).__init__(infile, outfile, *args, **kargs)

    @requires("bcftools")
    def _method_bcftools(self, *args, **kwargs):
        """Here we use the bcftools tool from samtools.

        `bcftools documentation <https://samtools.github.io/bcftools/bcftools.html>`_"""

        # -O, --output-type b|u|z|v Output compressed BCF (b), uncompressed BCF
        # (u), compressed VCF (z), uncompressed VCF (v). Use the -Ou option when
        # piping between bcftools subcommands to speed up performance
        cmd = "bcftools view {} -O v -o {}".format(self.infile, self.outfile)
        self.execute(cmd)