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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`FASTA` to :term:`TWOBIT` format"""
import colorlog
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
_log = colorlog.getLogger(__name__)
__all__ = ["FASTA2TWOBIT"]
[docs]class FASTA2TWOBIT(ConvBase):
"""Converts a sequence alignment in :term:`FASTA` format to :term:`TWOBIT` format
Methods available are based on UCSC faToTwoBit [UCSC]_.
"""
#: default value
_default_method = "ucsc"
def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs):
""".. rubric:: constructor
:param str infile: input :term:`FASTA` file.
:param str outfile: (optional) output :term:`TWOBIT` file
"""
super(FASTA2TWOBIT, self).__init__(infile, outfile)
[docs] @requires("faToTwoBit")
@compressor
def _method_ucsc(self, *args, **kwargs):
"""Convert fasta file in twobit format using ucsc faToTwoBit.
`uscsc faToTwoBit Documentation <https://genome.ucsc.edu/goldenPath/help/twoBit.html>`_"""
cmd = "faToTwoBit {infile} {outfile}".format(infile=self.infile, outfile=self.outfile)
self.execute(cmd)