def __init__(self, infile, outfile=None, alphabet=None, *args, **kwargs): """.. rubric:: constructor :param str infile: input :term:`PHYLIP` file. :param str outfile: (optional) output :term:`FASTA` file """ if not outfile: outfile = generate_outfile_name(infile, 'fasta') super().__init__(infile, outfile) self.alphabet = alphabet self._default_method = 'biopython'
def test_generate_outfile_name(): assert generate_outfile_name('foo.fasta', 'phylip') == 'foo.phylip' assert generate_outfile_name('/foo/bar.ext.fasta', 'clustal') == '/foo/bar.ext.clustal'