# This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Unittests for Bio.Align.Applications interface for MAFFT.""" import sys import os import unittest import subprocess from Bio import MissingExternalDependencyError from Bio.Align.Applications import MafftCommandline # Try to avoid problems when the OS is in another language os.environ["LANG"] = "C" mafft_exe = None if sys.platform == "win32": raise MissingExternalDependencyError( "Testing with MAFFT not implemented on Windows yet" ) else: from subprocess import getoutput output = getoutput("mafft -help") if "not found" not in output and "not recognized" not in output: if "MAFFT" in output: mafft_exe = "mafft" if not mafft_exe: raise MissingExternalDependencyError( "Install MAFFT if you want to use the Bio.Align.Applications wrapper." ) def check_mafft_version(mafft_exe): child = subprocess.Popen( "%s --help" % mafft_exe, stdout=subprocess.PIPE, stderr=subprocess.PIPE, universal_newlines=True, shell=(sys.platform != "win32"), ) stdoutdata, stderrdata = child.communicate() output = stdoutdata + "\n" + stderrdata return_code = child.returncode del child if ( "correctly installed?" in output or "mafft binaries have to be installed" in output ): raise MissingExternalDependencyError( "MAFFT does not seem to be correctly installed." ) # e.g. "MAFFT version 5.732 (2005/09/14)\n" # e.g. " MAFFT v6.717b (2009/12/03)\n" for marker in ["MAFFT version", "MAFFT v"]: index = output.find(marker) if index == -1: continue version = output[index + len(marker) :].strip().split(None, 1)[0] major = int(version.split(".", 1)[0]) if major < 6: raise MissingExternalDependencyError( "Test requires MAFFT v6 or later (found %s)." % version ) return (major, version) raise MissingExternalDependencyError("Couldn't determine MAFFT version.") # This also checks it actually runs! version_major, version_string = check_mafft_version(mafft_exe) class MafftApplication(unittest.TestCase): def setUp(self): self.infile1 = "Fasta/f002" def tearDown(self): if os.path.isfile("Fasta/f002.tree"): os.remove("Fasta/f002.tree") def test_Mafft_simple(self): """Simple round-trip through app with infile, result passed to stdout.""" # Use a keyword argument at init, cmdline = MafftCommandline(mafft_exe, input=self.infile1) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdoutdata, stderrdata = cmdline() self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680")) # Used to get "Progressive alignment ..." but in v7.245 # became "Progressive alignment 1/2..." and "Progressive alignment 2/2..." self.assertTrue( ("Progressive alignment ..." in stderrdata) or ("Progressive alignment 1/" in stderrdata), stderrdata, ) self.assertNotIn("$#=0", stderrdata) def test_Mafft_with_options(self): """Simple round-trip through app with infile and options, result passed to stdout.""" cmdline = MafftCommandline(mafft_exe) cmdline.set_parameter("input", self.infile1) cmdline.set_parameter("maxiterate", 100) cmdline.set_parameter("--localpair", True) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdoutdata, stderrdata = cmdline() self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680")) self.assertNotIn("$#=0", stderrdata) 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.assertNotIn("$#=0", stderrdata) if version_major >= 7: def test_Mafft_with_PHYLIP_output(self): """Simple round-trip through app with PHYLIP output.""" cmdline = MafftCommandline(mafft_exe, input=self.infile1, phylipout=True) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) stdoutdata, stderrdata = cmdline() # e.g. " 3 706\n" or " 3 681" but allow some variation in the column count self.assertTrue( stdoutdata.startswith(" 3 68") or stdoutdata.startswith(" 3 69") or stdoutdata.startswith(" 3 70"), stdoutdata, ) self.assertIn("gi|1348912 ", stdoutdata, stdoutdata) self.assertNotIn("gi|1348912|gb|G26680|G26680", stdoutdata, stdoutdata) self.assertNotIn("$#=0", 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" or " 3 681" but allow some variation in the column count self.assertTrue( stdoutdata.startswith(" 3 68") or stdoutdata.startswith(" 3 69") or stdoutdata.startswith(" 3 70"), stdoutdata, ) self.assertIn("gi|1348912|gb|G26680|G26680", stdoutdata, stdoutdata) self.assertNotIn("$#=0", stderrdata) def test_Mafft_with_complex_command_line(self): """Round-trip with complex command line.""" cmdline = MafftCommandline(mafft_exe) cmdline.set_parameter("input", self.infile1) cmdline.set_parameter("--localpair", True) cmdline.set_parameter("--weighti", 4.2) cmdline.set_parameter("retree", 5) cmdline.set_parameter("maxiterate", 200) cmdline.set_parameter("--nofft", True) cmdline.set_parameter("op", 2.04) cmdline.set_parameter("--ep", 0.51) cmdline.set_parameter("--lop", 0.233) cmdline.set_parameter("lep", 0.2) cmdline.set_parameter("--reorder", True) cmdline.set_parameter("--treeout", True) cmdline.set_parameter("nuc", True) self.assertEqual(str(eval(repr(cmdline))), str(cmdline)) self.assertEqual( str(cmdline), mafft_exe + " --localpair --weighti 4.2 --retree 5 " + "--maxiterate 200 --nofft --op 2.04 --ep 0.51" + " --lop 0.233 --lep 0.2 --reorder --treeout" + " --nuc Fasta/f002", ) stdoutdata, stderrdata = cmdline() self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680")) self.assertNotIn("$#=0", stderrdata) if __name__ == "__main__": runner = unittest.TextTestRunner(verbosity=2) unittest.main(testRunner=runner)