# #START_LICENSE###########################################################
#
#
# This file is part of the Environment for Tree Exploration program
# (ETE). http://etetoolkit.org
#
# ETE is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ETE is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY
# or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public
# License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ETE. If not, see .
#
#
# ABOUT THE ETE PACKAGE
# =====================
#
# ETE is distributed under the GPL copyleft license (2008-2015).
#
# If you make use of ETE in published work, please cite:
#
# Jaime Huerta-Cepas, Joaquin Dopazo and Toni Gabaldon.
# ETE: a python Environment for Tree Exploration. Jaime BMC
# Bioinformatics 2010,:24doi:10.1186/1471-2105-11-24
#
# Note that extra references to the specific methods implemented in
# the toolkit may be available in the documentation.
#
# More info at http://etetoolkit.org. Contact: huerta@embl.de
#
#
# #END_LICENSE#############################################################
#!/usr/bin/python
import unittest
from ..evol import EvolTree
from random import random as rnd
from copy import deepcopy
import os
from six.moves.cPickle import load, dump
import hashlib
DATAPATH = os.path.abspath(os.path.split(os.path.realpath(__file__))[0])+"/ete_evol_data/"
WRKDIR = DATAPATH + '/protamine/PRM1/'
BINDIR = os.getcwd() + '/bin/'
print(BINDIR)
def random_swap(tree):
'''
swap randomly tree, to make sure labelling as paml is well done
'''
for node in tree.iter_descendants():
if int (rnd()*100)%3:
node.swap_children()
def check_annotation (tree):
'''
check each node is labelled with a node_id
'''
for node in tree.iter_descendants():
if not hasattr (node, 'node_id'):
raise Exception ('Error, unable to label with paml ids')
return True
def which(program):
def is_exe(fpath):
return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
fpath, fname = os.path.split(program)
if fpath:
if is_exe(program):
return program
else:
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
class TestEvolEvolTree(unittest.TestCase):
"""Tests EvolTree basics"""
def test_paml_parser(self):
alignments = [' 3 6\nseq1\tyo\nATGATG\nseq2\nCTGATG\nseq3\nATGTTT\n',
' 3 6\n>seq1\nATGATG\n>seq2\t|prout\nCTGATG\n>seq3\nATGTTT\n',
'>seq1 \nATGATG\n>seq2\nCTGATG\n>seq3\nATGTTT\n']
for ali in alignments:
t = EvolTree('((seq1,seq2),seq3);')
t.link_to_alignment(ali)
self.assertEqual((t & 'seq1').nt_sequence, 'ATGATG')
self.assertEqual((t & 'seq2').nt_sequence, 'CTGATG')
self.assertEqual((t & 'seq3').nt_sequence, 'ATGTTT')
def test_load_model(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'protamine/PRM1/paml/'
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
tree.link_to_evol_model (WRKDIR + 'paml/M1/M1.out', 'M1')
tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2')
tree.link_to_evol_model (WRKDIR + 'paml/M7/M7.out', 'M7')
tree.link_to_evol_model (WRKDIR + 'paml/M8/M8.out', 'M8')
tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali')
self.assertEqual(sorted(tree._models.keys()),
sorted(['fb', 'M1', 'M2', 'M7', 'M8']))
self.assertEqual(len (tree.get_evol_model('M2').branches), 194)
self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569)
self.assert_('proportions' in str(tree.get_evol_model('M2')))
self.assert_('p2=' in str(tree.get_evol_model('M2')))
self.assert_('proportions' not in str(tree.get_evol_model('fb')))
self.assert_(' #193' in str(tree.get_evol_model('fb')))
def test_get_most_likely(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'protamine/PRM1/paml/'
tree.link_to_evol_model (WRKDIR + 'paml/M1/M1.out', 'M1')
tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2')
self.assertEqual(round(tree.get_most_likely ('M2','M1'),16),
round(6.3280740347111373e-10,16))
def test_labelling_tree(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'protamine/PRM1/paml/'
random_swap(tree)
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
self.assert_(check_annotation (tree))
def test_deep_copy(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'protamine/PRM1/paml/'
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
fba = deepcopy (tree.get_evol_model('fb'))
tree._models['fb.a'] = fba
self.assertEqual(str(tree.get_evol_model('fb.a')),
str(tree.get_evol_model('fb'))
)
def test_call_histface(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'protamine/PRM1/paml/'
tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali')
tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2.a')
col = {'NS' : 'grey', 'RX' : 'black',
'RX+': 'grey', 'CN' : 'black',
'CN+': 'grey', 'PS' : 'black', 'PS+': 'black'}
col2 = {'NS' : 'white', 'RX' : 'white',
'RX+': 'white', 'CN' : 'white',
'CN+': 'white', 'PS' : 'white', 'PS+': 'white'}
M2a = tree.get_evol_model('M2.a')
try:
import PyQt4
except ImportError:
pass
else:
M2a.set_histface (up=False, kind='stick', hlines=[1.0, 0.3],
hlines_col=['red','grey'], header='ugliest face')
M2a.set_histface (up=False, kind='curve', colors=col2,errors=True,
hlines = [2.5, 1.0, 4.0, 0.5],
header = 'Many lines, error boxes, background black',
hlines_col=['orange', 'yellow', 'red', 'cyan'])
M2a.set_histface (up=False, kind='bar', hlines = [1.0, 0.3],
hlines_col=['black','grey'],colors=col)
self.assertEqual(str(type(M2a.properties['histface'])),
"")
def test_run_codeml(self):
if which('codeml'):
tree = EvolTree('((seq1,seq2),seq3);')
tree.link_to_alignment('>seq1\nATGCTG\n>seq2\nATGCTG\n>seq3\nTTGATG\n')
tree.run_model('fb')
self.assert_('CODONML' in tree.get_evol_model('fb').run)
self.assert_('Time used:' in tree.get_evol_model('fb').run)
self.assert_('end of tree file' in tree.get_evol_model('fb').run)
self.assert_('lnL' in tree.get_evol_model('fb').run)
self.assert_(tree.get_descendants()[0].w > 0)
def test_run_slr(self):
if which('Slr'):
tree = EvolTree('((seq1,seq2),seq3);')
tree.link_to_alignment('>seq1\nCTGATTCTT\n>seq2\nCTGATTCTT\n>seq3\nATGATTCTT\n')
tree.run_model('SLR')
print(tree.get_evol_model('SLR').run)
self.assert_('Sitewise Likelihood R' in tree.get_evol_model('SLR').run)
self.assert_('Positively selected s' in tree.get_evol_model('SLR').run)
self.assert_('Conserved sites' in tree.get_evol_model('SLR').run)
self.assert_('lnL' in tree.get_evol_model('SLR').run)
def test_marking_trees(self):
TREE_PATH = DATAPATH + '/S_example/'
tree = EvolTree (TREE_PATH + 'tree.nw')
self.assertEqual(tree.write(),
'((Hylobates_lar,(Gorilla_gorilla,Pan_troglodytes)),Papio_cynocephalus);')
tree.mark_tree ([1, 3, 7] + [2, 6], marks=['#1']*3 + ['#2']*2, verbose=True)
self.assertEqual(tree.write().replace(' ', ''),
'((Hylobates_lar#2,(Gorilla_gorilla#1,Pan_troglodytes#1)#1)#2,Papio_cynocephalus);')
tree.mark_tree ([x.node_id for x in tree.get_descendants()],
marks=[''] * len (tree.get_descendants()), verbose=False)
self.assertEqual(tree.write().replace(' ', ''),
'((Hylobates_lar,(Gorilla_gorilla,Pan_troglodytes)),Papio_cynocephalus);')
def test_pickling(self):
tree = EvolTree(WRKDIR + 'tree.nw')
tree.workdir = DATAPATH + '/protamine/PRM1/paml/'
tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali')
tree.link_to_evol_model(WRKDIR + 'paml/M2/M2.out', 'M2.a')
out = open('blip.pik', 'wb')
dump(tree, out)
out.close()
out = open('blip.pik', 'rb')
tree2 = load(out)
out.close()
os.remove('blip.pik')
tree2_output = hashlib.md5(str(tree2.get_evol_model('M2.a')).encode()).hexdigest()
tree_output = hashlib.md5(str(tree.get_evol_model ('M2.a')).encode()).hexdigest()
self.assertEqual(tree_output, tree2_output)
if __name__ == '__main__':
unittest.main()