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#!/usr/bin/python
"""
10 Nov 2010
example to test, extrernal runs of codeml
"""
__author__ = "Francois-Jose Serra"
__email__ = "francois@barrabin.org"
__licence__ = "GPLv3"
__version__ = "0.0"
from ete3 import EvolTree, faces
from random import random as rnd
WRKDIR = 'data/protamine/PRM1/'
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: \n')
print(tree.get_most_likely ('M2','M1'))
print('pv of LRT M8 vs M7: \n')
print(tree.get_most_likely ('M8','M7'))
tree.show (histfaces=['M2'])
print('The End.')
def random_swap(tree):
for node in tree.iter_descendants():
if int (rnd()*100)%3:
node.swap_children()
def check_annotation (tree):
for node in tree.iter_descendants():
if not hasattr (node, 'paml_id'):
print('Error, unable to label with paml ids')
break
print('Labelling ok!')
if __name__ == "__main__":
exit(main())
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