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# Copyright (C) 2011, 2019 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 yn00 module."""
import unittest
import os
import os.path
from Bio.Phylo.PAML import yn00
from Bio.Phylo.PAML._paml import PamlError
import glob
class ModTest(unittest.TestCase):
align_dir = os.path.join("PAML", "Alignments")
tree_dir = os.path.join("PAML", "Trees")
ctl_dir = os.path.join("PAML", "Control_files")
results_dir = os.path.join("PAML", "Results")
working_dir = os.path.join("PAML", "yn00_test")
align_file = os.path.join(align_dir, "alignment.phylip")
dotname_align_file = os.path.join(align_dir, "alignment_dottednames.phylip")
out_file = os.path.join(results_dir, "test.out")
results_file = os.path.join(results_dir, "bad_results.out")
bad_ctl_file1 = os.path.join(ctl_dir, "bad1.ctl")
bad_ctl_file2 = os.path.join(ctl_dir, "bad2.ctl")
ctl_file = os.path.join(ctl_dir, "yn00", "yn00.ctl")
def tearDown(self):
"""Just in case yn00 creates some junk files, do a clean-up."""
del_files = [self.out_file, "2YN.dN", "2YN.dS", "2YN.t", "rst", "rst1", "rub"]
for filename in del_files:
if os.path.exists(filename):
os.remove(filename)
if os.path.exists(self.working_dir):
for filename in os.listdir(self.working_dir):
filepath = os.path.join(self.working_dir, filename)
os.remove(filepath)
os.rmdir(self.working_dir)
def setUp(self):
self.yn00 = yn00.Yn00()
def testAlignmentFileIsValid(self):
self.assertRaises((AttributeError, TypeError, OSError), yn00.Yn00, alignment=[])
self.yn00.alignment = []
self.yn00.out_file = self.out_file
self.assertRaises((AttributeError, TypeError, OSError), self.yn00.run)
def testAlignmentExists(self):
self.assertRaises(
(EnvironmentError, IOError), yn00.Yn00, alignment="nonexistent"
)
self.yn00.alignment = "nonexistent"
self.yn00.out_file = self.out_file
self.assertRaises(IOError, self.yn00.run)
def testWorkingDirValid(self):
self.yn00.alignment = self.align_file
self.yn00.out_file = self.out_file
self.yn00.working_dir = []
self.assertRaises((AttributeError, TypeError, OSError), self.yn00.run)
def testOptionExists(self):
self.assertRaises((AttributeError, KeyError), self.yn00.set_options, xxxx=1)
self.assertRaises((AttributeError, KeyError), self.yn00.get_option, "xxxx")
def testAlignmentSpecified(self):
self.yn00.out_file = self.out_file
self.assertRaises((AttributeError, ValueError), self.yn00.run)
def testOutputFileSpecified(self):
self.yn00.alignment = self.align_file
self.assertRaises((AttributeError, ValueError), self.yn00.run)
# def testPamlErrorsCaught(self):
# self.yn00.alignment = self.align_file
# self.yn00.out_file = self.out_file
# self.assertRaises((EnvironmentError, PamlError),
# self.yn00.run)
def testCtlFileValidOnRun(self):
self.yn00.alignment = self.align_file
self.yn00.out_file = self.out_file
self.assertRaises(
(AttributeError, TypeError, OSError), self.yn00.run, ctl_file=[]
)
def testCtlFileExistsOnRun(self):
self.yn00.alignment = self.align_file
self.yn00.out_file = self.out_file
self.assertRaises(IOError, self.yn00.run, ctl_file="nonexistent")
def testCtlFileValidOnRead(self):
self.assertRaises(
(AttributeError, TypeError, OSError), self.yn00.read_ctl_file, []
)
self.assertRaises(
(AttributeError, KeyError), self.yn00.read_ctl_file, self.bad_ctl_file1
)
self.assertRaises(AttributeError, self.yn00.read_ctl_file, self.bad_ctl_file2)
target_options = {
"verbose": 1,
"icode": 0,
"weighting": 0,
"commonf3x4": 0,
"ndata": 1,
}
self.yn00.read_ctl_file(self.ctl_file)
self.assertEqual(self.yn00._options, target_options)
def testCtlFileExistsOnRead(self):
self.assertRaises(IOError, self.yn00.read_ctl_file, ctl_file="nonexistent")
def testResultsValid(self):
self.assertRaises((AttributeError, TypeError, OSError), yn00.read, [])
def testResultsExist(self):
self.assertRaises((EnvironmentError, IOError), yn00.read, "nonexistent")
def testResultsParsable(self):
self.assertRaises(ValueError, yn00.read, self.results_file)
def testParseAllVersions(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
self.assertEqual(len(results), 5)
self.assertEqual(len(results["Homo_sapie"]), 4)
self.assertEqual(len(results["Homo_sapie"]["Pan_troglo"]), 5)
def testParseLongNames(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00_long-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 7)
# ...each of which is compared to the other six.
self.assertEqual({len(v) for v in results.values()}, {6})
# ...each of which has five measures.
self.assertEqual(
{len(v) for taxa in results.values() for v in taxa.values()}, {5}
)
def testParseDottedNames(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00_dotted-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 5)
# ...each of which is compared to the other six.
self.assertEqual({len(v) for v in results.values()}, {4})
# ...each of which has five measures.
self.assertEqual(
{len(v) for taxa in results.values() for v in taxa.values()}, {5}
)
self.assertEqual(len(results["Homo.sapie"]), 4)
self.assertEqual(len(results["Homo.sapie"]["Pan.troglo"]), 5)
def testParseDottedNumNames(self):
pattern = os.path.join(self.results_dir, "yn00", "yn00_dottednum-*")
for results_file in glob.glob(pattern):
results = yn00.read(results_file)
# Expect seven taxa...
self.assertEqual(len(results), 7)
# ...each of which is compared to the other six.
self.assertEqual({len(v) for v in results.values()}, {6})
# ...each of which has five measures.
self.assertEqual(
{len(v) for taxa in results.values() for v in taxa.values()}, {5}
)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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