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# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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 unittest
import os
import sys
from Bio.Phylo.PAML import codeml, baseml, yn00
from Bio import MissingExternalDependencyError
def is_exe(filepath):
"""Test if a file is an executable."""
return os.path.exists(filepath) and os.access(filepath, os.X_OK)
def which(program):
"""Find the path to an executable."""
filepath, filename = os.path.split(program)
os_path = os.environ["PATH"].split(os.pathsep)
if sys.platform == "win32":
try:
# This can vary depending on the Windows language.
prog_files = os.environ["PROGRAMFILES"]
except KeyError:
prog_files = r"C:\Program Files"
# For Windows, the user is instructed to move the programs to a folder
# and then to add the folder to the system path. Just in case they didn't
# do that, we can check for it in Program Files.
likely_dirs = ["", # Current dir
prog_files,
os.path.join(prog_files, "paml41"),
os.path.join(prog_files, "paml43"),
os.path.join(prog_files, "paml44"),
os.path.join(prog_files, "paml45")] + sys.path
os_path.extend(likely_dirs)
for path in os.environ["PATH"].split(os.pathsep):
exe_file = os.path.join(path, program)
if is_exe(exe_file):
return exe_file
return None
# Find the PAML binaries
if sys.platform == "win32":
binaries = ["codeml.exe", "baseml.exe", "yn00.exe"]
else:
binaries = ["codeml", "baseml", "yn00"]
for binary in binaries:
if which(binary) is None:
raise MissingExternalDependencyError(
"Install PAML if you want to use the Bio.Phylo.PAML wrapper.")
class Common(unittest.TestCase):
"""Base class for PAML unit tests."""
del_files = []
def __del__(self):
"""Just in case tool creates some junk files, do a clean-up."""
del_files = self.del_files
for filename in del_files:
if os.path.exists(filename):
os.remove(filename)
class CodemlTest(Common):
"""Tests for PAML tool codeml."""
def setUp(self):
self.cml = codeml.Codeml()
def testCodemlBinary(self):
"""Test that the codeml binary runs and generates correct output
and is the correct version.
"""
ctl_file = os.path.join("PAML", "Control_files", "codeml", "codeml.ctl")
self.cml.read_ctl_file(ctl_file)
self.cml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
self.cml.tree = os.path.join("PAML", "Trees", "species.tree")
self.cml.out_file = os.path.join("PAML", "temp.out")
self.cml.working_dir = os.path.join("PAML", "codeml_test")
results = self.cml.run()
self.assertTrue(results["version"] > "4.0")
self.assertTrue("NSsites" in results)
self.assertEqual(len(results["NSsites"]), 1)
self.assertEqual(len(results["NSsites"][0]), 5)
class BasemlTest(Common):
"""Tests for PAML tool baseml."""
def setUp(self):
self.bml = baseml.Baseml()
def testBasemlBinary(self):
"""Test that the baseml binary runs and generates correct output
and is the correct version.
"""
ctl_file = os.path.join("PAML", "Control_files", "baseml", "baseml.ctl")
self.bml.read_ctl_file(ctl_file)
self.bml.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
self.bml.tree = os.path.join("PAML", "Trees", "species.tree")
self.bml.out_file = os.path.join("PAML", "temp.out")
self.bml.working_dir = os.path.join("PAML", "baseml_test")
results = self.bml.run()
self.assertTrue(results["version"] > "4.0")
self.assertTrue("parameters" in results)
self.assertEqual(len(results["parameters"]), 5)
class Yn00Test(Common):
"""Tests for PAML tool yn00."""
def setUp(self):
self.yn = yn00.Yn00()
def testYn00Binary(self):
"""Test that the yn00 binary runs and generates correct output.
yn00 output does not specify the version number.
"""
ctl_file = os.path.join("PAML", "Control_files", "yn00", "yn00.ctl")
self.yn.read_ctl_file(ctl_file)
self.yn.alignment = os.path.join("PAML", "Alignments", "alignment.phylip")
self.yn.out_file = os.path.join("PAML", "temp.out")
self.yn.working_dir = os.path.join("PAML", "yn00_test")
results = self.yn.run()
self.assertEqual(len(results), 5)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
clean_up()
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