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) raw_input(" ====> hit some key to see the Tree with alignment") T.show() ### # run free-branch model, and display result print '\n\n\n ----> We define now our working directory, that will be created:', \ WORKING_PATH T.workdir = (WORKING_PATH) print '\n ----> and run the free-branch model with run_model function:\n\n%s\n%s\n%s\n'\ % ('*'*10 + ' doc ' + '*'*10, T.run_model.func_doc, '*'*30) raw_input(" ====> Hit some key to start free-branch computation with codeml...\n") T.run_model('fb') T.show() ### # run site model, and display result
from ete2.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')