def test_run_slr(self): if which('Slr'): tree = EvolTree('((seq1,seq2),seq3);') tree.link_to_alignment('>seq1\nCTGATTCTT\n>seq2\nCTGATTCTT\n>seq3\nATGATTCTT\n') tree.run_model('SLR') self.assert_('Sitewise Likelihood R' in tree.get_evol_model('SLR').run) self.assert_('Positively selected s' in tree.get_evol_model('SLR').run) self.assert_('Conserved sites' in tree.get_evol_model('SLR').run) self.assert_('lnL' in tree.get_evol_model('SLR').run)
def test_run_codeml(self): if which('codeml'): tree = EvolTree('((seq1,seq2),seq3);') tree.link_to_alignment('>seq1\nATGCTG\n>seq2\nATGCTG\n>seq3\nTTGATG\n') tree.run_model('fb') self.assert_('CODONML' in tree.get_evol_model('fb').run) self.assert_('Time used:' in tree.get_evol_model('fb').run) self.assert_('end of tree file' in tree.get_evol_model('fb').run) self.assert_('lnL' in tree.get_evol_model('fb').run) self.assert_(tree.get_descendants()[0].w > 0)
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 print '\n\n\n ----> We are now goingn to run sites model M1 and M2 with run_model function:\n' raw_input(" ====> hit some key to start") for model in ['M1', 'M2']: print 'running model ' + model T.run_model(model) print '\n\n\n ----> and use the get_most_likely function to compute the LRT between those models:\n' print 'get_most_likely function: \n\n'+ '*'*10 + ' doc ' + '*'*10 print '\n' + T.get_most_likely.func_doc print '*'*30