File: test_phyml_tool.py

package info (click to toggle)
python-biopython 1.68+dfsg-3~bpo8+1
  • links: PTS, VCS
  • area: main
  • in suites: jessie-backports
  • size: 46,856 kB
  • sloc: python: 160,306; xml: 93,216; ansic: 9,118; sql: 1,208; makefile: 155; sh: 63
file content (69 lines) | stat: -rw-r--r-- 2,265 bytes parent folder | download | duplicates (2)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
# Copyright (C) 2012 by Eric Talevich.
# 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.

"""Unit tests for Bio.Phylo.Applications wrappers."""

import sys
import os
import unittest

from Bio import Phylo
from Bio.Phylo.Applications import PhymlCommandline
from Bio import MissingExternalDependencyError

# Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'

phyml_exe = None
exe_name = "PhyML-3.1_win32.exe" if sys.platform == "win32" else "phyml"
from Bio._py3k import getoutput
try:
    output = getoutput(exe_name + " --version")
    if "not found" not in output and "20" in output:
        phyml_exe = exe_name
except OSError:
    # TODO: Use FileNotFoundError once we drop Python 2
    # Python 2.6 or 2.7 on Windows XP:
    # WindowsError: [Error 2] The system cannot find the file specified
    # Python 3.3 or 3.4 on Windows XP:
    # FileNotFoundError: [WinError 2] The system cannot find the file specified
    pass

if not phyml_exe:
    raise MissingExternalDependencyError(
        "Install PhyML 3.0 if you want to use the Bio.Phylo.Applications wrapper.")


# Example Phylip file with 4 aligned protein sequences
EX_PHYLIP = 'Phylip/interlaced2.phy'


class AppTests(unittest.TestCase):
    """Tests for application wrappers."""

    def test_phyml(self):
        """Run PhyML using the wrapper."""
        cmd = PhymlCommandline(phyml_exe, input=EX_PHYLIP, datatype='aa')
        # Smoke test
        try:
            out, err = cmd()
            self.assertTrue(len(out) > 0)
            self.assertEqual(len(err), 0)
            # Check the output tree
            tree = Phylo.read(EX_PHYLIP + '_phyml_tree', 'newick')
            self.assertEqual(tree.count_terminals(), 4)
        finally:
            # Clean up generated files
            for suffix in ['_phyml_tree.txt', '_phyml_stats.txt']:
                fname = EX_PHYLIP + suffix
                if os.path.isfile(fname):
                    os.remove(fname)


# ---------------------------------------------------------

if __name__ == '__main__':
    runner = unittest.TextTestRunner(verbosity=2)
    unittest.main(testRunner=runner)