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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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"""Conversion from :term:`TWOBIT` to :term:`FASTA` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import requires
_log = colorlog.getLogger(__name__)
__all__ = ["TWOBIT2FASTA"]
[docs]class TWOBIT2FASTA(ConvBase):
"""Converts a sequence alignment in :term:`TWOBIT` format to :term:`FASTA` format
Conversion is based on UCSC [UCSC]_ and py2bit.
"""
#: Default value
_default_method = "py2bit"
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`TWOBIT` file.
:param str outfile: (optional) output :term:`FASTA` file
"""
super(TWOBIT2FASTA, self).__init__(infile, outfile)
self.alphabet = alphabet
[docs] @requires("twoBitToFa")
def _method_ucsc(self, *args, **kwargs):
"""Convert twobit file in fasta format using ucsc twobittofa.
`uscsc faToTwoBit Documentation <https://genome.ucsc.edu/goldenPath/help/twoBit.html>`_"""
cmd = "twoBitToFa {infile} {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)
# py2bit is from deeptols repo
[docs] @requires(python_library="py2bit")
def _method_py2bit(self, *args, **kwargs):
"""This method uses the py2bit python extension.
`py2bit documentation <https://github.com/deeptools/py2bit>`_"""
import py2bit
data = py2bit.open(self.infile)
with open(self.outfile, "w") as fout:
for chrom in sorted(data.chroms()):
seq = data.sequence(chrom)
fout.write(">{}\n{}\n".format(chrom, seq))