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# Copyright 2009 by David Winter. All rights reserved.
# 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 os
import sys
import unittest
import subprocess
from Bio import MissingExternalDependencyError
from Bio import AlignIO
from Bio.Nexus import Trees # One day we should use planned TreeIO module
from Bio.Emboss.Applications import FDNADistCommandline, FNeighborCommandline
from Bio.Emboss.Applications import FSeqBootCommandline, FProtDistCommandline
from Bio.Emboss.Applications import FProtParsCommandline, FConsenseCommandline
from Bio.Emboss.Applications import FTreeDistCommandline, FDNAParsCommandline
#Try to avoid problems when the OS is in another language
os.environ['LANG'] = 'C'
exes_wanted = ['fdnadist', 'fneighbor', 'fprotdist','fprotpars','fconsense',
'fseqboot', 'ftreedist', 'fdnapars']
exes = dict() #Dictionary mapping from names to exe locations
if "EMBOSS_ROOT" in os.environ:
#Windows default installation path is C:\mEMBOSS which contains the exes.
#EMBOSS also sets an environment variable which we will check for.
path = os.environ["EMBOSS_ROOT"]
if os.path.isdir(path):
for name in exes_wanted:
if os.path.isfile(os.path.join(path, name+".exe")):
exes[name] = os.path.join(path, name+".exe")
del path, name
if sys.platform!="win32":
import commands
for name in exes_wanted:
#This will "just work" if installed on the path as normal on Unix
output = commands.getoutput("%s -help" % name)
if "not found" not in output and "not recognized" not in output:
exes[name] = name
del output
del name
if len(exes) < len(exes_wanted):
raise MissingExternalDependencyError(\
"Install the Emboss package 'PhylipNew' if you want to use the "+\
"Bio.Emboss.Applications wrappers for phylogenetic tools.")
###########################################################################
# A few top level functions that are called repeatedly in the test cases
def write_AlignIO_dna():
"""Convert opuntia.aln to a phylip file"""
assert 1 == AlignIO.convert("Clustalw/opuntia.aln", "clustal",
"Phylip/opuntia.phy", "phylip")
def write_AlignIO_protein():
"""Convert hedgehog.aln to a phylip file"""
assert 1 == AlignIO.convert("Clustalw/hedgehog.aln", "clustal",
"Phylip/hedgehog.phy", "phylip")
def clean_up():
"""Delete tests files (to be used as tearDown() function in test fixtures)"""
for filename in ["test_file", "Phylip/opuntia.phy","Phylip/hedgehog.phy"]:
if os.path.isfile(filename):
os.remove(filename)
def parse_trees(filename):
"""Helper function until we have Bio.Phylo on trunk."""
data = open("test_file", "r").read()
for tree_str in data.split(";\n"):
if tree_str:
yield Trees.Tree(tree_str+";")
class DistanceTests(unittest.TestCase):
"""Tests for calculating distance based phylogenetic trees with phylip"""
def tearDown(self):
clean_up()
test_taxa = ['Archaeohip', 'Calippus', 'Hypohippus', 'M._secundu',
'Merychippu', 'Mesohippus', 'Nannipus', 'Neohippari',
'Parahippus', 'Pliohippus']
def distances_from_alignment(self, filename, DNA = True):
"""check we can make distance matrix from a given alignment"""
self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
if DNA:
cline = FDNADistCommandline(exes["fdnadist"],
method = 'j',
sequence= filename,
outfile = "test_file",
auto = True)
else:
cline = FProtDistCommandline(exes["fprotdist"],
method = 'j',
sequence= filename,
outfile = "test_file",
auto = True)
stdout, strerr = cline()
#biopython can't grok distance matrices, so we'll just check it exists
self.assertTrue(os.path.isfile("test_file"))
def tree_from_distances(self, filename):
"""Check we can estimate a tree from a distance matrix"""
self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
cline = FNeighborCommandline(exes["fneighbor"],
datafile = filename,
outtreefile = "test_file",
auto= True, filter = True)
stdout, stderr = cline()
for tree in parse_trees("test_file"):
tree_taxa = [t.replace(" ", "_") for t in tree.get_taxa()]
self.assertEqual(self.test_taxa, sorted(tree_taxa))
def test_distances_from_phylip_DNA(self):
"""Calculate a distance matrix from an phylip alignment"""
self.distances_from_alignment("Phylip/horses.phy")
def test_distances_from_AlignIO_DNA(self):
"""Calculate a distance matrix from an alignment written by AlignIO"""
write_AlignIO_dna()
self.distances_from_alignment("Phylip/opuntia.phy")
#def test_distances_from_bootstrapped_phylip_DNA(self):
# """Calculate a set of distance matrices from phylip alignments"""
# self.distances_from_alignment("Phylip/bs_horses.phy")
# fprotdist tests
def test_distances_from_protein_phylip(self):
"""Calculate a distance matrix from phylip protein alignment"""
self.distances_from_alignment("Phylip/interlaced.phy", DNA=False)
def test_distances_from_protein_AlignIO(self):
"""Calculate distance matrix from an AlignIO written protein alignment"""
write_AlignIO_protein()
self.distances_from_alignment("Phylip/hedgehog.phy", DNA=False)
#def test_distances_from_bootstrapped_phylip_protein(self):
# """Calculate distance matrices from a bootstrapped protein alignment"""
# self.distances_from_alignment("Clustalw/bs_interlaced.phy", DNA=False)
# fneighbor tests
#def test_tree_from_distances(self):
# """Estimate tree from distance matrix and parse it."""
# self.tree_from_distances("Phylip/horses.fdnadist")
# This one won't work because of a bug in EMBOSS 6.0.1
#def test_tree_from_bootstrapped_distances(self):
# """Estimate tree from bootstrapped distance matrix and parse it"""
# self.tree_from_distances("Phylip/bs_horses.fdnadist")
class ParsimonyTests(unittest.TestCase):
"""Tests for estimating parsimony based phylogenetic trees with phylip"""
def tearDown(self):
clean_up()
def parsimony_tree(self, filename, format, DNA=True):
"""Estimate a parsimony tree from an alignment"""
self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
if DNA:
cline = FDNAParsCommandline(exes["fdnapars"],
sequence = filename,
outtreefile = "test_file",
auto= True, stdout=True)
else:
cline = FProtParsCommandline(exes["fprotpars"],
sequence = filename,
outtreefile = "test_file",
auto= True, stdout=True)
stdout, stderr = cline()
a_taxa = [s.name.replace(" ", "_") for s in
AlignIO.parse(open(filename, "r"), format).next()]
for tree in parse_trees("test_file"):
t_taxa = [t.replace(" ", "_") for t in tree.get_taxa()]
self.assertEqual(sorted(a_taxa), sorted(t_taxa))
# fdnapars tests
#def test_parsimony_tree_from_phylip_DNA(self):
# """Make a parsimony tree from a phylip DNA alignment"""
# self.parsimony_tree("Phylip/horses.phy", "phylip")
def test_parsimony_tree_from_AlignIO_DNA(self):
"""Make a parsimony tree from an alignment written with AlignIO"""
write_AlignIO_dna()
self.parsimony_tree("Phylip/opuntia.phy", "phylip")
#def test_parsimony_bootstrapped_phylip_DNA(self):
# """Make a parsimony tree from a bootstrapped phylip DNA alignment"""
# self.parsimony_tree("Phylip/bs_horses.phy", "phylip")
# fprotpars tests
#def test_parsimony_tree_from_phylip_protein(self):
# """Make a parsimony tree from a phylip DNA alignment"""
# self.parsimony_tree("Phylip/interlaced.phy", "phylip", DNA=False)
def test_parsimony_from_AlignIO_protein(self):
"""Make a parsimony tree from protein alignment written with AlignIO"""
write_AlignIO_protein()
self.parsimony_tree("Phylip/interlaced.phy", "phylip", DNA=False)
#def test_parsimony_tree_bootstrapped_phylip_protein(self):
# """Make a parsimony tree from a phylip DNA alignment"""
# self.parsimony_tree("Phylip/bs_interlaced.phy", "phylip", DNA=False)
class BootstrapTests(unittest.TestCase):
"""Tests for pseudosampling alignments with fseqboot"""
def tearDown(self):
clean_up()
def check_bootstrap(self, filename, format, align_type="d"):
"""Check we can use fseqboot to pseudosample an alignment
The align_type type argument is passed to the commandline object to
set the output format to use (from [D]na,[p]rotein and [r]na )
"""
self.assertTrue(os.path.isfile(filename), "Missing %s" % filename)
cline = FSeqBootCommandline(exes["fseqboot"],
sequence = filename,
outfile = "test_file",
seqtype = align_type,
reps = 2,
auto = True, filter = True)
stdout, stderr = cline()
# the resultant file should have 2 alignments...
bs = list(AlignIO.parse(open("test_file", "r" ), format))
self.assertEqual(len(bs), 2)
# ..and each name in the original alignment...
a_names = [s.name.replace(" ", "_") for s in
AlignIO.read(open(filename, "r"), format)]
# ...should be in each alignment in the bootstrapped file
for a in bs:
self.assertEqual(a_names, [s.name.replace(" ", "_") for s in a])
def test_bootstrap_phylip_DNA(self):
"""Pseudosample a phylip DNA alignment"""
self.check_bootstrap("Phylip/horses.phy", "phylip")
def test_bootstrap_AlignIO_DNA(self):
"""Pseudosample a phylip DNA alignment written with AlignIO"""
write_AlignIO_dna()
self.check_bootstrap("Phylip/opuntia.phy", "phylip")
def test_bootstrap_phylip_protein(self):
"""Pseudosample a phylip protein alignment"""
self.check_bootstrap("Phylip/interlaced.phy", "phylip", "p")
def test_bootstrap_AlignIO_protein(self):
"""Pseudosample a phylip protein alignment written with AlignIO"""
write_AlignIO_protein()
self.check_bootstrap("Phylip/hedgehog.phy", "phylip", "p")
class TreeComparisonTests(unittest.TestCase):
"""Tests for comparing phylogenetic trees with phylip tools"""
def tearDown(self):
clean_up()
def test_fconsense(self):
"""Calculate a consensus tree with fconsense"""
cline = FConsenseCommandline(exes["fconsense"],
intreefile = "Phylip/horses.tree",
outtreefile = "test_file",
auto = True, filter = True)
stdout, stderr = cline()
#Split the next and get_taxa into two steps to help 2to3 work
tree1 = parse_trees("test_file").next()
taxa1 = tree1.get_taxa()
for tree in parse_trees("Phylip/horses.tree"):
taxa2 = tree.get_taxa()
self.assertEqual(sorted(taxa1),sorted(taxa2))
def test_ftreedist(self):
"""Calculate the distance between trees with ftreedist"""
cline = FTreeDistCommandline(exes["ftreedist"],
intreefile = "Phylip/horses.tree",
outfile = "test_file",
auto = True, filter = True)
stdout, stderr = cline()
self.assertTrue(os.path.isfile("test_file"))
if __name__ == "__main__":
runner = unittest.TextTestRunner(verbosity = 2)
unittest.main(testRunner=runner)
clean_up()
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