def METHOD_NAME(self):
    """Round-trip through app and read clustalw alignment from file."""
    cmdline = TCoffeeCommandline(t_coffee_exe, gapopen=-2)
    cmdline.infile = self.infile1
    cmdline.outfile = self.outfile4
    cmdline.set_parameter("output", "clustalw_aln")
    cmdline.outorder = "input"
    cmdline.set_parameter("gapext", -5)
    cmdline.type = "protein"
    self.assertEqual(
        str(cmdline),
        t_coffee_exe
        + " -output clustalw_aln -infile Fasta/fa01 -outfile Fasta/tc_out.aln "
        "-type protein -outorder input -gapopen -2 -gapext -5",
    )
    stdout, stderr = cmdline()
    self.assertTrue(stderr.strip().startswith("PROGRAM: T-COFFEE"))
    align = AlignIO.read(self.outfile4, "clustal")
    records = list(SeqIO.parse(self.infile1, "fasta"))
    self.assertEqual(len(records), len(align))
    for old, new in zip(records, align):
        self.assertEqual(old.id, new.id)
        self.assertEqual(
            str(new.seq).replace("-", ""), str(old.seq).replace("-", "")
        )