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# Bioconvert is a project to facilitate the interconversion #
# of life science data from one format to another. #
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"""Convert :term:`BIGWIG` to :term:`BEDGRAPH` format """
import colorlog
import pyBigWig
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ["BIGWIG2BEDGRAPH"]
[docs]class BIGWIG2BEDGRAPH(ConvBase):
"""Converts a sequence alignment in :term:`BIGWIG` format to :term:`BEDGRAPH` format
Conversion is based on ucsc bigWigToBedGraph tool or pybigwig (default)
[DEEPTOOLS]_.
"""
#: Default value
_default_method = "pybigwig"
def __init__(self, infile, outfile): # =None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`BIGWIG` file.
:param str outfile: (optional) output :term:`BEDGRAPH` file
"""
super(BIGWIG2BEDGRAPH, self).__init__(infile, outfile)
# self.alphabet = alphabet
[docs] @requires("bigWigToBedGraph")
def _method_ucsc(self, *args, **kwargs):
"""Convert bigwig file in bedgraph format using ucsc tool.
`ucsc.bedgraph documentation <https://genome.ucsc.edu/goldenPath/help/bedgraph.html>`_"""
cmd = "bigWigToBedGraph {infile} {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)
[docs] @requires(python_library="pyBigWig")
def _method_pybigwig(self, *args, **kwargs):
"""In this method we use the python extension written in C, pyBigWig.
`pyBigWig documentation <https://github.com/deeptools/pyBigWig>`_"""
bw = pyBigWig.open(self.infile)
assert bw.isBigWig() is True, "Not a valid bigWig file"
with open(self.outfile, "w") as fout:
for chrom in bw.chroms():
for tup in bw.intervals(chrom):
s, e, val = tup
if int(val) == val:
val = int(val)
fout.write("{}\t{}\t{}\t{}\n".format(chrom, s, e, val))