Exemplos de EvolTree.link_to_evol_model em Python

Exemplo n.º 1

Arquivo: test_protamine.py Projeto: razib764/Treelib

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.'

Exemplo n.º 2

Arquivo: test_protamine.py Projeto: AlishaMechtley/ete

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.'

Exemplo n.º 3

'can be run from within a paml directory'
from ete3 import EvolTree
import os

tree_file = "testTree.tre"
alignment_file = "testAlignment.fasta"
model = "./model/out"
model_name = "bsD.bl_0.2w"
# model_name = os.path.basename(os.getcwd())

testTree = EvolTree(tree_file)
testTree.link_to_alignment(alignment_file)
testTree.link_to_evol_model(model, model_name)

testTree.show()