test_PAML_tools.py

# 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.

"""Tests for PAML tools module."""

import os
import sys
import unittest

from Bio import MissingExternalDependencyError
from Bio.Phylo.PAML import baseml
from Bio.Phylo.PAML import codeml
from Bio.Phylo.PAML import yn00


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):
        """Check codeml runs, 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.assertGreater(results["version"], "4.0")
        self.assertIn("NSsites", 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):
        """Check baseml runs, 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.assertGreater(results["version"], "4.0")
        self.assertIn("parameters", 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):
        """Check 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)