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# Bioconvert is a project to facilitate the interconversion #
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"""Convert :term:`EMBL` file to :term:`GENBANK` format"""
from bioconvert import ConvBase
from bioconvert.core.decorators import compressor, requires
__all__ = ["EMBL2GENBANK"]
[docs]class EMBL2GENBANK(ConvBase):
"""Convert :term:`EMBL` file to :term:`GENBANK` file
Methods available are based on squizz [SQUIZZ]_ and
biopython [BIOPYTHON]_.
"""
#: Default value
_default_method = "biopython"
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input EMBL file
:param str outfile: output GENBANK filename
"""
super(EMBL2GENBANK, self).__init__(infile, outfile, *args, **kargs)
[docs] @requires(external_binary="squizz")
@compressor
def _method_squizz(self, *args, **kwargs):
"""Header is less informative than the one obtained with biopython."""
cmd = "squizz -f embl -c genbank {} > {} ".format(self.infile, self.outfile)
self.execute(cmd)
[docs] @requires(python_library="biopython")
@compressor
def _method_biopython(self, *args, **kwargs):
"""For this method we use the biopython package Bio.SeqIO.
`Bio.SeqIO Documentation <https://biopython.org/docs/1.76/api/Bio.SeqIO.html>`_"""
from Bio import SeqIO
SeqIO.convert(self.infile, "embl", self.outfile, "genbank")