###########################################################################
# 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, #
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# GNU General Public License for more details. #
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# 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/>. #
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# Repository: https://github.com/bioconvert/bioconvert #
# Documentation: http://bioconvert.readthedocs.io #
###########################################################################
"""Convert :term:`BAM` format to :term:`BEDGRAPH` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ["BAM2BEDGRAPH"]
[docs]class BAM2BEDGRAPH(ConvBase):
"""Convert sorted :term:`BAM` file into :term:`BEDGRAPH` file
Compute the coverage (depth) in BEDGRAPH.
Regions with zero coverage are also reported.
Note that this BEDGRAPH format is of the form::
chrom chromStart chromEnd dataValue
Note that consecutive positions with same values are compressed.
::
chr1 0 75 0
chr1 75 176 1
chr1 176 177 2
.. warning:: the BAM file must be sorted. This can be achieved with
bamtools.
Methods available are based on bedtools [BEDTOOLS]_ and mosdepth
[MOSDEPTH]_.
"""
# 4 minutes with bedtools and 20s with mosdepth
#: Default value
_default_method = "bedtools"
_threading = True
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("mosdepth")
def _method_mosdepth(self, *args, **kwargs):
"""Do the conversion using mosdepth.
`mosdepth documentation <https://github.com/brentp/mosdepth>`_"""
# For testing, we need to save into a specific temporary directory
import tempfile
with tempfile.TemporaryDirectory() as tmpdir:
try:
cmd = "mosdepth {}/.bioconvert -t {} {}".format(tmpdir, self.threads, self.infile)
self.execute(cmd)
if self.outfile.endswith(".gz"):
pass
else:
cmd = "gunzip -c {}/.bioconvert.per-base.bed.gz > {}".format(tmpdir, self.outfile)
self.execute(cmd)
except Exception as err:
raise (err)
finally:
cmd = "rm -f {name}/.bioconvert.per-base.bed.gz {name}/.bioconvert.per-base.bed.gz.csi"
cmd += " {name}/.bioconvert.mosdepth.global.dist.txt"
self.execute(cmd.format(name=tmpdir))