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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`BIGBED` format to :term:`BED` format """
import colorlog
import pyBigWig
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ["BIGBED2BED"]
[docs]class BIGBED2BED(ConvBase):
"""Converts a sequence alignment in :term:`BIGBED` format to :term:`BED4` format
Methods available are based on pybigwig [DEEPTOOLS]_.
"""
#: Default value
_default_method = "pybigwig"
def __init__(self, infile, outfile): # =None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`BIGBED` file.
:param str outfile: (optional) output :term:`BED4` file
"""
super(BIGBED2BED, self).__init__(infile, outfile)
[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.isBigBed() is True, "Not a valid bigBed file"
with open(self.outfile, "w") as fout:
for chrom in sorted(bw.chroms().keys()):
L = bw.chroms()[chrom]
for tup in bw.entries(chrom, 0, L):
s, e, val = tup
# the bigbed may have many columns. We consider only bed4
# for now
# FIXME
try:
val = val.split("\t")[0]
except:
pass
fout.write("{}\t{}\t{}\t{}\n".format(chrom, s, e, val))