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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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"""Convert :term:`GENBANK` to :term:`GFF3` format"""
from bioconvert import ConvBase
__all__ = ["GENBANK2GFF3"]
[docs]class GENBANK2GFF3(ConvBase):
"""Convert :term:`GENBANK` file to :term:`GFF3` file
Method based on biocode.
"""
#: Default value
_default_method = "biocode"
def __init__(self, infile, outfile, *args, **kargs):
""".. rubric:: constructor
:param str infile: input GENBANK file
:param str outfile: output GFF3 filename
"""
super(GENBANK2GFF3, self).__init__(infile, outfile)
[docs] def _method_biocode(self, *args, **kwargs):
"""Uses scripts from biocode copied and modified in bioconvert.utils.biocode
Please see `Main entry <https://github.com/jorvis/biocode/>`_
"""
from bioconvert.utils.biocode.convert_genbank_to_gff3 import gbk2gff3
gbk2gff3(self.infile, self.outfile, fasta=False)