Source code for bioconvert.bam2cov

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# Bioconvert is a project to facilitate the interconversion               #
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"""Convert :term:`BAM` format to :term:`COV` format"""
import colorlog

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

_log = colorlog.getLogger(__name__)

__all__ = ["BAM2COV"]


[docs]class BAM2COV(ConvBase):
    """Convert sorted :term:`BAM` file into :term:`COV` file


    Note that the COV format is of the form::

        chr1    1   0
        chr1    2   0
        chr1    3   0
        chr1    4   0
        chr1    5   0

    that is contig name, position, coverage.

    .. warning:: the BAM file must be sorted. This can be achieved with
        bamtools using *bamtools sort -in INPUT.bam*

    Methods available are based on samtools [SAMTOOLS]_ or bedtools [BEDTOOLS]_.
    """

    #: Default value
    # _default_method = "samtools"
    _default_method = "bedtools"

    def __init__(self, infile, outfile):
        """.. rubric:: Constructor

        :param str infile: The path to the input BAM file. **It must be sorted**.
        :param str outfile: The path to the output file
        """
        super().__init__(infile, outfile)

[docs]    @requires("samtools")
    def _method_samtools(self, *args, **kwargs):
        """Do the conversion sorted :term:`BAM` -> :term:`BED` using samtools

        `SAMtools documentation <http://www.htslib.org/doc/samtools.html>`_"""
        cmd = "samtools depth -aa {} > {}".format(self.infile, self.outfile)
        self.execute(cmd)

[docs]    @requires("bedtools")
    def _method_bedtools(self, *args, **kwargs):
        """Do the conversion sorted :term:`BAM` -> :term:`BED` using bedtools

        `bedtools documentation <https://bedtools.readthedocs.io/en/latest/>`_"""
        cmd = "bedtools genomecov -d -ibam {} > {}".format(self.infile, self.outfile)
        self.execute(cmd)