def test_get_most_likely(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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_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_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_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_marking_trees(self):
TREE_PATH = ETEPATH + '/examples/evol/data/S_example/'
tree = EvolTree (TREE_PATH + 'measuring_S_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 (map (lambda x: x.node_id, 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_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')
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_call_histface(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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'])),
"<class 'ete_dev.treeview.faces.SequencePlotFace'>")
def test_deep_copy(self):
tree = EvolTree(WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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_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')
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_call_histface(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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'])),
"<class 'ete_dev.treeview.faces.SequencePlotFace'>")
def test_deep_copy(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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_get_most_likely(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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_pickling(self):
tree = EvolTree(WRKDIR + 'tree.nw')
tree.workdir = ETEPATH + '/examples/data/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', 'w')
dump(tree, out)
out.close()
out = open('blip.pik')
tree2 = load(out)
out.close()
os.remove('blip.pik')
self.assertEqual(str(tree2.get_evol_model('M2.a')),
str(tree.get_evol_model('M2.a')))
def test_pickling(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = ETEPATH + '/examples/data/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', 'w')
dump (tree, out)
out.close()
out = open('blip.pik')
tree2 = load (out)
out.close()
os.remove('blip.pik')
self.assertEqual(str(tree2.get_evol_model('M2.a')),
str(tree.get_evol_model('M2.a'))
)
def get_ctrl_keys():
'''
given a model name returns table in html format of
parameters given to paml
'''
tree = EvolTree()
ctrl_table = 'var all_models = {'
for model in AVAIL:
m = Model(model, tree)
ctrl_table += "'" + model + "': ["
for line in m.get_ctrl_string().split('\n')[4:]:
if not line:
continue
if '*' in line:
line = line.split()[1] + '=' + line.split()[0]
param, value = map(lambda x: x.strip(), line.split('='))
#ctrl_table += '<tr><td>%s</td><td>%s</td></tr>' % (param, value)
ctrl_table += "'%s'," % (param)
ctrl_table = ctrl_table[:-1]
ctrl_table += "],"
return ctrl_table[:-1] + '};'
def get_ctrl_string():
'''
given a model name returns table in html format of
parameters given to paml
'''
tree = EvolTree()
ctrl_table = 'var all_models = {'
for model in AVAIL:
m = Model(model, tree)
ctrl_table += "'" + model + "':'<tr>"
for i, line in enumerate(m.get_ctrl_string().split('\n')[4:]):
if not line:
continue
if '*' in line:
line = line.split()[1] + '=' + line.split()[0]
param, value = map(lambda x: x.strip(), line.split('='))
#ctrl_table += '<tr><td>%s</td><td>%s</td></tr>' % (param, value)
ctrl_table += '<td><font size=1> %s </font></td><td><font size=1> <input typ=text id=%s size=4 value=%s></font></td>' % (
param, param, value)
if (i + 1) % 3 == 0:
ctrl_table += '</tr><tr>'
ctrl_table += "</tr>',"
return ctrl_table[:-1] + '};'
def my_tree_loader(tree):
""" This is function is used to load trees within the
WebTreeApplication object. """
t = EvolTree(tree, sp_naming_function=extract_species_code)
application.set_img_properties(None)
return t
#MY_PATH = '/home/francisco/toolbox/ete2-codeml/doc/tutorial/examples/'
MY_PATH = ''
TREE_PATH = MY_PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = MY_PATH + re.sub('\./', '', ALG_PATH )
###
# load tree
print '\n ----> we create a EvolTree object, and give to him a topology, from',
print TREE_PATH
out = True
while out == True:
try:
T = EvolTree(TREE_PATH)
out = False
except:
sys.stderr.write('Bad path for working directory. Enter new path or quit("Q"):\n')
PATH = raw_input('')
if PATH.startswith('q') or PATH.startswith('Q'):
sys.exit()
TREE_PATH = "./measuring_%s_tree.nw" % (typ)
ALG_PATH = "./alignment_%s_measuring_evol.fasta" % (typ)
TREE_PATH = PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = PATH + re.sub('\./', '', ALG_PATH )
print T
print '\n ----> and an alignment from: \n'+ALG_PATH+'\n\n'
T.link_to_alignment(ALG_PATH)
def test_labelling_tree(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/protamine/PRM1/paml/'
random_swap(tree)
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
self.assert_(check_annotation (tree))
def test_load_model(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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')))
from ete_dev.evol import EvolTree
import sys, re
typ = 'S'
#while typ != 'L' and typ != 'S':
# typ = raw_input (\
# "choose kind of example [L]ong or [S]hort, hit [L] or [S]:\n")
TREE_PATH = "data/S_example/measuring_%s_tree.nw" % (typ)
ALG_PATH = "data/S_example/alignment_%s_measuring_evol.fasta" % (typ)
WORKING_PATH = "data/S_example/paml/"
MY_PATH = ''
TREE_PATH = MY_PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = MY_PATH + re.sub('\./', '', ALG_PATH )
T = EvolTree (TREE_PATH)
T.link_to_alignment (ALG_PATH)
T.workdir = (WORKING_PATH)
T.link_to_evol_model(T.workdir + '/fb/out','fb')
T.link_to_evol_model(T.workdir + '/M1/out','M1')
T.link_to_evol_model(T.workdir + '/M2/out','M2')
T.show(histfaces=['M2'])
sys.stderr.write('\n\nThe End.\n\n')
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_marking_trees(self):
TREE_PATH = 'examples/evol/data/S_example/'
tree = EvolTree (TREE_PATH + 'measuring_S_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 (map (lambda x: x.node_id, 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_load_model(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/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_labelling_tree(self):
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'examples/evol/data/protamine/PRM1/paml/'
random_swap(tree)
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
self.assert_(check_annotation (tree))
def main():
"""
main function
"""
tree = EvolTree (WRKDIR + 'tree.nw')
tree.workdir = 'data/protamine/PRM1/paml/'
random_swap(tree)
tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb')
check_annotation (tree)
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')
print 'pv of LRT M2 vs M1: ',
print tree.get_most_likely ('M2','M1')
print 'pv of LRT M8 vs M7: ',
print tree.get_most_likely ('M8','M7')
tree.show (histfaces=['M2'])
print 'The End.'
# Author: Francois-Jose Serra
# Creation Date: 2010/04/26 17:17:06
from ete_dev.evol import EvolTree
import sys, re
typ = 'S'
#while typ != 'L' and typ != 'S':
# typ = raw_input (\
# "choose kind of example [L]ong or [S]hort, hit [L] or [S]:\n")
TREE_PATH = "data/S_example/measuring_%s_tree.nw" % (typ)
ALG_PATH = "data/S_example/alignment_%s_measuring_evol.fasta" % (typ)
WORKING_PATH = "data/S_example/paml/"
MY_PATH = ''
TREE_PATH = MY_PATH + re.sub('\./', '', TREE_PATH)
ALG_PATH = MY_PATH + re.sub('\./', '', ALG_PATH)
T = EvolTree(TREE_PATH)
T.link_to_alignment(ALG_PATH)
T.workdir = (WORKING_PATH)
T.link_to_evol_model(T.workdir + '/fb/out', 'fb')
T.link_to_evol_model(T.workdir + '/M1/out', 'M1')
T.link_to_evol_model(T.workdir + '/M2/out', 'M2')
T.show(histfaces=['M2'])
sys.stderr.write('\n\nThe End.\n\n')