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Test mafft --namelength

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peterjc committed Jul 8, 2013
1 parent 2d16161 commit ae61932c6db18874e9210a93cb9708282ac9e64b
Showing with 16 additions and 0 deletions.
  1. +16 −0 Tests/test_Mafft_tool.py
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@@ -121,6 +121,22 @@ def test_Mafft_with_PHYLIP_output(self):
stdoutdata, stderrdata = cmdline()
#e.g. " 3 706\n" but allow some variation in the column count
self.assertTrue(stdoutdata.startswith(" 3 70"), stdoutdata)
+ self.assertTrue("gi|1348912 " in stdoutdata,
+ stdoutdata)
+ self.assertTrue("gi|1348912|gb|G26680|G26680" not in stdoutdata,
+ stdoutdata)
+ self.assertTrue("$#=0" not in stderrdata)
+
+ def test_Mafft_with_PHYLIP_namelength(self):
+ """Check PHYLIP with --namelength"""
+ cmdline = MafftCommandline(mafft_exe, input=self.infile1,
+ phylipout=True, namelength=50)
+ self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
+ stdoutdata, stderrdata = cmdline()
+ #e.g. " 3 706\n" but allow some variation in the column count
+ self.assertTrue(stdoutdata.startswith(" 3 70"), stdoutdata)
+ self.assertTrue("gi|1348912|gb|G26680|G26680" in stdoutdata,
+ stdoutdata)
self.assertTrue("$#=0" not in stderrdata)
def test_Mafft_with_complex_command_line(self):

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