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.'
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.'
'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()