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Sourcecode: python-biopython version File versions  Download package

Simple round-trip through app with clustal output

Definition at line 99 of file test_Mafft_tool.py.

References test_Dialign_tool.DialignApplication.infile1, and test_Mafft_tool.MafftApplication.infile1.

    def test_Mafft_with_Clustalw_output(self):
        """Simple round-trip through app with clustal output"""
        cmdline = MafftCommandline(mafft_exe)
        #Use some properties:
        cmdline.input = self.infile1
        cmdline.clustalout = True
        self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
        stdoutdata, stderrdata = cmdline()
        #e.g. "CLUSTAL format alignment by MAFFT ..."
        #or "CLUSTAL (-like) formatted alignment by MAFFT FFT-NS-2 (v6.240)"
        self.assertTrue(stdoutdata.startswith("CLUSTAL"), stdoutdata)
        self.assertTrue("$#=0" not in stderrdata)

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