###########################################################################
# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
# #
# Copyright © 2018-2022 Institut Pasteur, Paris and CNRS. #
# #
# bioconvert is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# bioconvert is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details. #
# #
# You should have received a copy of the GNU General Public License #
# along with this program (COPYING file). #
# If not, see <http://www.gnu.org/licenses/>. #
# #
# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Convert :term:`BEDGRAPH` to :term:`BIGWIG` format"""
import os
import colorlog
from bioconvert.core.base import ConvArg, ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ["BEDGRAPH2BIGWIG"]
[docs]class BEDGRAPH2BIGWIG(ConvBase):
"""Converts :term:`BEDGRAPH` format to :term:`BIGWIG` format
Conversion is based on bedGraph2BigWig tool. Note that an
argument --chrom-sizes is required.
"""
#: Default value
_default_method = "ucsc"
def __init__(self, infile, outfile): # , alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`BEDGRAPH` file.
:param str outfile: (optional) output :term:`BIGWIG` file
"""
super(BEDGRAPH2BIGWIG, self).__init__(infile, outfile)
[docs] @requires("bedGraphToBigWig")
def _method_ucsc(self, *args, **kwargs):
"""Convert bedgraph file in bigwig format using ucsc tool.
`bigWig documentation <https://genome.ucsc.edu/goldenpath/help/bigWig.html>`_
`chromosome size <http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes>`_"""
chrom_sizes = kwargs.get("chrom_sizes", None)
if chrom_sizes is None:
raise ValueError("Must provide --chrom-sizes option")
cmd = "bedGraphToBigWig {infile} {chrom_sizes} {outfile}".format(
infile=self.infile, outfile=self.outfile, chrom_sizes=chrom_sizes
)
self.execute(cmd)
@classmethod
def get_additional_arguments(cls):
yield ConvArg(
names="--chrom-sizes",
default=None,
help="a two-column file/URL: <chromosome name> <size in bases>",
)