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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
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.
"""
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 Bio._py3k import getoutput
output = getoutput("mafft -help")
if "not found" not in output and "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.assertTrue("$#=0" not in stderrdata)
def test_Mafft_with_options(self):
"""Simple round-trip through app with infile and options.
Result passed to stdout.
"""
cmdline = MafftCommandline(mafft_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("maxiterate", 100)
cmdline.set_parameter("--localpair", True)
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdoutdata, stderrdata = cmdline()
self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680"))
self.assertTrue("$#=0" not in 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.assertTrue("$#=0" not in stderrdata)
if version_major >= 7:
def test_Mafft_with_PHYLIP_output(self):
"""Simple round-trip through app with PHYLIP output"""
cmdline = MafftCommandline(mafft_exe, input=self.infile1,
phylipout=True)
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
stdoutdata, stderrdata = cmdline()
# e.g. " 3 706\n" or " 3 681" but allow some variation in the column count
self.assertTrue(stdoutdata.startswith(" 3 68") or
stdoutdata.startswith(" 3 69") or
stdoutdata.startswith(" 3 70"), stdoutdata)
self.assertTrue("gi|1348912 " in stdoutdata,
stdoutdata)
self.assertTrue("gi|1348912|gb|G26680|G26680" not in stdoutdata,
stdoutdata)
self.assertTrue("$#=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" 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.assertTrue("gi|1348912|gb|G26680|G26680" in stdoutdata,
stdoutdata)
self.assertTrue("$#=0" not in stderrdata)
def test_Mafft_with_complex_command_line(self):
"""Round-trip with complex command line."""
cmdline = MafftCommandline(mafft_exe)
cmdline.set_parameter("input", self.infile1)
cmdline.set_parameter("--localpair", True)
cmdline.set_parameter("--weighti", 4.2)
cmdline.set_parameter("retree", 5)
cmdline.set_parameter("maxiterate", 200)
cmdline.set_parameter("--nofft", True)
cmdline.set_parameter("op", 2.04)
cmdline.set_parameter("--ep", 0.51)
cmdline.set_parameter("--lop", 0.233)
cmdline.set_parameter("lep", 0.2)
cmdline.set_parameter("--reorder", True)
cmdline.set_parameter("--treeout", True)
cmdline.set_parameter("nuc", True)
self.assertEqual(str(eval(repr(cmdline))), str(cmdline))
self.assertEqual(str(cmdline), mafft_exe +
" --localpair --weighti 4.2 --retree 5 " +
"--maxiterate 200 --nofft --op 2.04 --ep 0.51" +
" --lop 0.233 --lep 0.2 --reorder --treeout" +
" --nuc Fasta/f002")
stdoutdata, stderrdata = cmdline()
self.assertTrue(stdoutdata.startswith(">gi|1348912|gb|G26680|G26680"))
self.assertTrue("$#=0" not in stderrdata)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)