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#!/usr/bin/python
"""
15 Nov 2010
example to illustrate use of sites model, displaying and comparison
"""
__author__ = "Francois-Jose Serra"
__email__ = "francois@barrabin.org"
__licence__ = "GPLv3"
__version__ = "0.0"
from ete3 import EvolTree
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print (tree)
try:
input = raw_input
except NameError:
pass
eval(input ('\n tree and alignment loaded\n Hit some key, to start computation of site models M1 and M2.\n'))
print ('running model M1')
tree.run_model ('M1')
print ('running model M2')
tree.run_model ('M2')
print('\n\n comparison of models M1 and M2, p-value: ' + str(tree.get_most_likely ('M2','M1')))
#tree.show()
print ('by default the hist represented is this one:')
tree.show (histfaces=['M2'])
print ('but we can choose between many others...')
model2 = tree.get_evol_model ('M2')
col2 = {'NS' : 'black', 'RX' : 'black',
'RX+': 'black', 'CN' : 'black',
'CN+': 'black', 'PS' : 'black', 'PS+': 'black'}
model2.set_histface (up=False, kind='curve', colors=col2, ylim=[0,4], hlines = [2.5, 1.0, 4.0, 0.5], header = 'Many lines, error boxes, background black',
hlines_col=['orange', 'yellow', 'red', 'cyan'], errors=True)
tree.show(histfaces=['M2'])
model2.set_histface (up=False, kind='stick', hlines = [1.0,0.3], hlines_col=['black','grey'])
tree.show(histfaces=['M2'])
col = {'NS' : 'grey', 'RX' : 'black',
'RX+': 'grey', 'CN' : 'black',
'CN+': 'grey', 'PS' : 'black', 'PS+': 'black'}
model2.set_histface (up=False, kind='bar', colors=col, hlines=[1.0,0.3], hlines_col=['black','grey'])
tree.show(histfaces=['M2'])
print ('running model M7')
tree.run_model ('M7')
print ('running positive selection model M8')
tree.run_model ('M8')
print ('running relaxation model M8a')
tree.run_model ('M8a')
print ('running model M3')
tree.run_model ('M3')
print('\n\n comparison of models M7 and M8, p-value: ' + str(tree.get_most_likely ('M8','M7')))
print('\n\n comparison of models M8a and M8, p-value: ' + str(tree.get_most_likely ('M8','M8a')))
print ('The End.')
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