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test_Mafft_tool.py
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test_Mafft_tool.py
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# 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)