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|
# Copyright (C) 2011, 2015, 2016 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 os.path
from Bio.Phylo.PAML import codeml
from Bio.Phylo.PAML._paml import PamlError
# Some constants to assist with testing:
# This is the number of parameters that should be parsed for each
# NSsites site class model
SITECLASS_PARAMS = {0: 6, 1: 4, 2: 4, 3: 4, 7: 5, 8: 8, 22: 4}
# This is the default number of site classes per NSsites site
# class model
SITECLASSES = {0: None, 1: 2, 2: 3, 3: 3, 7: 10, 8: 11, 22: 3}
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", "codeml_test")
align_file = os.path.join(align_dir, "alignment.phylip")
tree_file = os.path.join(tree_dir, "species.tree")
bad_tree_file = os.path.join(tree_dir, "bad.tree")
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")
bad_ctl_file3 = os.path.join(ctl_dir, "bad3.ctl")
ctl_file = os.path.join(ctl_dir, "codeml", "codeml.ctl")
def tearDown(self):
"""Just in case CODEML creates some junk files, do a clean-up."""
del_files = [self.out_file, "2NG.dN", "2NG.dS", "2NG.t", "codeml.ctl",
"lnf", "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.cml = codeml.Codeml()
def testAlignmentFileIsValid(self):
self.assertRaises((AttributeError, TypeError, OSError),
codeml.Codeml, alignment=list())
self.cml.alignment = list()
self.cml.tree = self.tree_file
self.cml.out_file = self.out_file
self.assertRaises((AttributeError, TypeError, OSError),
self.cml.run)
def testAlignmentExists(self):
self.assertRaises((EnvironmentError, IOError), codeml.Codeml,
alignment="nonexistent")
self.cml.alignment = "nonexistent"
self.cml.tree = self.tree_file
self.cml.out_file = self.out_file
self.assertRaises(IOError, self.cml.run)
def testTreeFileValid(self):
self.assertRaises((AttributeError, TypeError, OSError),
codeml.Codeml, tree=list())
self.cml.alignment = self.align_file
self.cml.tree = list()
self.cml.out_file = self.out_file
self.assertRaises((AttributeError, TypeError, OSError),
self.cml.run)
def testTreeExists(self):
self.assertRaises((EnvironmentError, IOError), codeml.Codeml,
tree="nonexistent")
self.cml.alignment = self.align_file
self.cml.tree = "nonexistent"
self.cml.out_file = self.out_file
self.assertRaises(IOError, self.cml.run)
def testWorkingDirValid(self):
self.cml.tree = self.tree_file
self.cml.alignment = self.align_file
self.cml.out_file = self.out_file
self.cml.working_dir = list()
self.assertRaises((AttributeError, TypeError, OSError),
self.cml.run)
def testOutputFileValid(self):
self.cml.tree = self.tree_file
self.cml.alignment = self.align_file
self.cml.out_file = list()
self.assertRaises((AttributeError, ValueError, OSError),
self.cml.run)
def testOptionExists(self):
self.assertRaises((AttributeError, KeyError),
self.cml.set_options, xxxx=1)
self.assertRaises((AttributeError, KeyError),
self.cml.get_option, "xxxx")
def testAlignmentSpecified(self):
self.cml.tree = self.tree_file
self.cml.out_file = self.out_file
self.assertRaises((AttributeError, ValueError),
self.cml.run)
def testTreeSpecified(self):
self.cml.alignment = self.align_file
self.cml.out_file = self.out_file
self.assertRaises((AttributeError, ValueError),
self.cml.run)
def testOutputFileSpecified(self):
self.cml.alignment = self.align_file
self.cml.tree = self.tree_file
self.assertRaises((AttributeError, ValueError),
self.cml.run)
def testPamlErrorsCaught(self):
self.cml.alignment = self.align_file
self.cml.tree = self.bad_tree_file
self.cml.out_file = self.out_file
self.assertRaises((EnvironmentError, PamlError),
self.cml.run)
def testCtlFileValidOnRun(self):
self.cml.alignment = self.align_file
self.cml.tree = self.tree_file
self.cml.out_file = self.out_file
self.assertRaises((AttributeError, TypeError, OSError),
self.cml.run, ctl_file=list())
def testCtlFileExistsOnRun(self):
self.cml.alignment = self.align_file
self.cml.tree = self.tree_file
self.cml.out_file = self.out_file
self.assertRaises((EnvironmentError, IOError),
self.cml.run, ctl_file="nonexistent")
def testCtlFileValidOnRead(self):
self.assertRaises((AttributeError, TypeError, OSError),
self.cml.read_ctl_file, list())
self.assertRaises((AttributeError, KeyError),
self.cml.read_ctl_file, self.bad_ctl_file1)
self.assertRaises(AttributeError,
self.cml.read_ctl_file, self.bad_ctl_file2)
self.assertRaises(TypeError,
self.cml.read_ctl_file, self.bad_ctl_file3)
target_options = {"noisy": 0,
"verbose": 0,
"runmode": 0,
"seqtype": 1,
"CodonFreq": 2,
"ndata": None,
"clock": 0,
"aaDist": None,
"aaRatefile": None,
"model": 0,
"NSsites": [0],
"icode": 0,
"Mgene": 0,
"fix_kappa": 0,
"kappa": 4.54006,
"fix_omega": 0,
"omega": 1,
"fix_alpha": 1,
"alpha": 0,
"Malpha": 0,
"ncatG": None,
"getSE": 0,
"RateAncestor": 0,
"Small_Diff": None,
"cleandata": 1,
"fix_blength": 1,
"method": 0,
"rho": None,
"fix_rho": None}
self.cml.read_ctl_file(self.ctl_file)
# Compare the dictionary keys:
self.assertEqual(sorted(self.cml._options), sorted(target_options))
for key in target_options:
self.assertEqual(self.cml._options[key], target_options[key],
"%s: %r vs %r"
% (key, self.cml._options[key], target_options[key]))
def testCtlFileExistsOnRead(self):
self.assertRaises((EnvironmentError, IOError),
self.cml.read_ctl_file, ctl_file="nonexistent")
def testResultsValid(self):
self.assertRaises((AttributeError, TypeError, OSError),
codeml.read, list())
def testResultsExist(self):
self.assertRaises((EnvironmentError, IOError),
codeml.read, "nonexistent")
def testResultsParsable(self):
self.assertRaises(ValueError, codeml.read, self.results_file)
def testParseSEs(self):
res_dir = os.path.join(self.results_dir, "codeml", "SE")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
# Only site class model 0 was simulated
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(0 in models, version_msg)
model = models[0]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
# There should be one new item in the parameters, "SEs"
self.assertEqual(len(params), SITECLASS_PARAMS[0] + 1, version_msg)
self.assertTrue("SEs" in params, version_msg)
def testParseAllNSsites(self):
res_dir = os.path.join(self.results_dir, "codeml", "all_NSsites")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# There should be 4 top-level items: 'codon model', 'model',
# 'version', & 'NSsites'
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("NSsites" in results, version_msg)
# There should be 6 NSsites classes: 0, 1, 2, 3, 7 & 8
self.assertEqual(len(results["NSsites"]), 6, version_msg)
# Each site class model should have 5 sub-items: 'lnL', 'tree',
# 'description', 'parameters', & 'tree length'. It should
# have the correct number of parameters also.
for model_num in [0, 1, 2, 3, 7, 8]:
model = results["NSsites"][model_num]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
self.assertEqual(len(params), SITECLASS_PARAMS[model_num],
version_msg)
self.assertTrue("branches" in params, version_msg)
branches = params["branches"]
# There are 7 branches in the test case (specific to these
# test cases)
self.assertEqual(len(branches), 7, version_msg)
if "site classes" in params:
self.assertEqual(len(params["site classes"]),
SITECLASSES[model_num], version_msg)
def testParseNSsite3(self):
res_dir = os.path.join(self.results_dir, "codeml", "NSsite3")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# There should be 5 top-level items: 'codon model', 'model',
# 'version', 'NSsites' & site-class model, the last of which
# is only there when only one NSsites class is used
self.assertEqual(len(results), 5, version_msg)
self.assertTrue('site-class model' in results, version_msg)
self.assertEqual(results['site-class model'], 'discrete',
version_msg)
self.assertTrue("NSsites" in results, version_msg)
# There should be 1 NSsites classe: 3
self.assertEqual(len(results["NSsites"]), 1, version_msg)
# Each site class model should have 5 sub-items: 'lnL', 'tree',
# 'description', 'parameters', & 'tree length'. It should
# have the correct number of parameters also.
model = results["NSsites"][3]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
self.assertEqual(len(params), SITECLASS_PARAMS[3],
version)
self.assertTrue("site classes" in params, version_msg)
site_classes = params["site classes"]
self.assertEqual(len(site_classes), 4, version_msg)
def testParseBranchSiteA(self):
res_dir = os.path.join(self.results_dir, "codeml", "branchsiteA")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# There are 5 top-level items in this case:
# 'codon model', 'model', 'version', 'NSsites' & 'site-class model'
self.assertEqual(len(results), 5, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
# Only site class model 2 is simulated for Branch Site A
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(2 in models, version_msg)
model = models[2]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
# Branch Site A results lack a "branches" parameter
self.assertEqual(len(params), SITECLASS_PARAMS[2] - 1, version_msg)
self.assertTrue("site classes" in params, version_msg)
site_classes = params["site classes"]
# Branch Site A adds another site class
self.assertEqual(len(site_classes), SITECLASSES[2] + 1,
version)
for class_num in [0, 1, 2, 3]:
self.assertTrue(class_num in site_classes, version_msg)
site_class = site_classes[class_num]
self.assertEqual(len(site_class), 2, version_msg)
self.assertTrue("branch types" in site_class, version_msg)
branches = site_class["branch types"]
self.assertEqual(len(branches), 2, version_msg)
def testParseCladeModelC(self):
cladeC_res_dir = os.path.join(self.results_dir, "codeml",
"clademodelC")
for results_file in os.listdir(cladeC_res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(cladeC_res_dir, results_file)
results = codeml.read(results_path)
# 5 top-level items again in this case
self.assertEqual(len(results), 5, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
# Only site class model 2 is simulated for Clade Model C
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(2 in models, version_msg)
model = models[2]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
# Clade Model C results lack a "branches" parameter
self.assertEqual(len(params), SITECLASS_PARAMS[2] - 1, version_msg)
self.assertTrue("site classes" in params, version_msg)
site_classes = params["site classes"]
self.assertEqual(len(site_classes), SITECLASSES[2],
version)
for class_num in [0, 1, 2]:
self.assertTrue(class_num in site_classes, version_msg)
site_class = site_classes[class_num]
self.assertEqual(len(site_class), 2, version_msg)
self.assertTrue("branch types" in site_class, version_msg)
branches = site_class["branch types"]
self.assertEqual(len(branches), 2, version_msg)
def testParseNgene2Mgene02(self):
res_dir = os.path.join(self.results_dir, "codeml", "ngene2_mgene02")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(0 in models, version_msg)
model = models[0]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
# This type of model has fewer parameters for model 0
self.assertEqual(len(params), 4, version_msg)
self.assertTrue("rates" in params, version_msg)
rates = params["rates"]
self.assertEqual(len(rates), 2, version_msg)
def testParseNgene2Mgene1(self):
res_dir = os.path.join(self.results_dir, "codeml", "ngene2_mgene1")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("genes" in results, version_msg)
genes = results["genes"]
self.assertEqual(len(genes), 2, version_msg)
model = genes[0]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
self.assertEqual(len(params), SITECLASS_PARAMS[0], version_msg)
def testParseNgene2Mgene34(self):
res_dir = os.path.join(self.results_dir, "codeml", "ngene2_mgene34")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(0 in models, version_msg)
model = models[0]
self.assertEqual(len(model), 5, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
# This type of model has fewer parameters for model 0
self.assertEqual(len(params), 3, version_msg)
self.assertTrue("rates" in params, version_msg)
rates = params["rates"]
self.assertEqual(len(rates), 2, version_msg)
self.assertTrue("genes" in params, version_msg)
genes = params["genes"]
self.assertEqual(len(genes), 2, version_msg)
def testParseFreeRatio(self):
res_dir = os.path.join(self.results_dir, "codeml", "freeratio")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("NSsites" in results, version_msg)
models = results["NSsites"]
self.assertEqual(len(models), 1, version_msg)
self.assertTrue(0 in models, version_msg)
model = models[0]
# With the free ratio model, you get 3 extra trees: dN tree,
# dS tree and omega tree
self.assertEqual(len(model), 8, version_msg)
self.assertTrue("parameters" in model, version_msg)
params = model["parameters"]
self.assertEqual(len(params), SITECLASS_PARAMS[0], version_msg)
self.assertTrue("branches" in params, version_msg)
# There should be 7 branches
branches = params["branches"]
self.assertEqual(len(branches), 7, version_msg)
self.assertTrue("omega" in params, version_msg)
omega = params["omega"]
self.assertEqual(len(omega), 7, version_msg)
def testParsePairwise(self):
res_dir = os.path.join(self.results_dir, "codeml", "pairwise")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# Pairwise models have an extra top-level item: pairwise
self.assertEqual(len(results), 5, version_msg)
self.assertTrue("pairwise" in results, version_msg)
pairwise = results["pairwise"]
self.assertEqual(len(pairwise), 5, version_msg)
def testParseAA(self):
res_dir = os.path.join(self.results_dir, "codeml", "aa_model0")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# Amino Acid analysis has different top-levels:
# 'NSsites', 'model', 'version', 'lnL max', 'distances'
# Version 4.1 doesn't seem to produce distances in the results
if version == "4_1":
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("lnL max" in results, version_msg)
else:
self.assertEqual(len(results), 5, version_msg)
self.assertTrue("lnL max" in results, version_msg)
self.assertTrue("distances" in results, version_msg)
distances = results["distances"]
# non-pairwise AA analysis only gives raw distances
self.assertEqual(len(distances), 1, version_msg)
def testParseAAPairwise(self):
res_dir = os.path.join(self.results_dir, "codeml", "aa_pairwise")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
# Pairwise AA analysis has one top-level fewer than non-pairwise
self.assertEqual(len(results), 4, version_msg)
self.assertTrue("lnL max" in results, version_msg)
self.assertTrue("distances" in results, version_msg)
distances = results["distances"]
# Pairwise AA analysis has ML & raw distances
self.assertEqual(len(distances), 2, version_msg)
def testTreeParseVersatility(self):
"""Test finding trees in the results, in response to bug #453, where
trees like (A, (B, C)); weren't being caught"""
res_file = os.path.join(self.results_dir, "codeml",
"tree_regexp_versatility.out")
results = codeml.read(res_file)
self.assertTrue("NSsites" in results)
nssites = results["NSsites"]
self.assertTrue(0 in nssites)
m0 = nssites[0]
self.assertTrue("tree" in m0)
self.assertTrue(m0["tree"] is not None)
self.assertNotEqual(len(m0["tree"]), 0)
def testParseM2arel(self):
res_dir = os.path.join(self.results_dir, "codeml", "m2a_rel")
for results_file in os.listdir(res_dir):
version = results_file.split('-')[1].split('.')[0]
version_msg = "Improper parsing for version %s" \
% version.replace('_', '.')
results_path = os.path.join(res_dir, results_file)
results = codeml.read(results_path)
self.assertTrue("NSsites" in results)
self.assertTrue(22 in results["NSsites"])
model = results["NSsites"][22]
self.assertEqual(len(model), 5, version_msg)
params = model["parameters"]
self.assertEqual(len(params), SITECLASS_PARAMS[22],
version_msg)
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity=2)
unittest.main(testRunner=runner)
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