def test_call_histface(self): tree = EvolTree (WRKDIR + 'tree.nw') tree.workdir = 'examples/evol/data/protamine/PRM1/paml/' tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali') tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2.a') col = {'NS' : 'grey', 'RX' : 'black', 'RX+': 'grey', 'CN' : 'black', 'CN+': 'grey', 'PS' : 'black', 'PS+': 'black'} col2 = {'NS' : 'white', 'RX' : 'white', 'RX+': 'white', 'CN' : 'white', 'CN+': 'white', 'PS' : 'white', 'PS+': 'white'} M2a = tree.get_evol_model('M2.a') try: import PyQt4 except ImportError: pass else: M2a.set_histface (up=False, kind='stick', hlines=[1.0, 0.3], hlines_col=['red','grey'], header='ugliest face') M2a.set_histface (up=False, kind='curve', colors=col2,errors=True, hlines = [2.5, 1.0, 4.0, 0.5], header = 'Many lines, error boxes, background black', hlines_col=['orange', 'yellow', 'red', 'cyan']) M2a.set_histface (up=False, kind='bar', hlines = [1.0, 0.3], hlines_col=['black','grey'],colors=col) self.assertEqual(str(type(M2a.properties['histface'])), "<class 'ete2.treeview.faces.SequencePlotFace'>")
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_paml_parser(self): alignments = [' 3 6\nseq1\tyo\nATGATG\nseq2\nCTGATG\nseq3\nATGTTT\n', ' 3 6\n>seq1\nATGATG\n>seq2\t|prout\nCTGATG\n>seq3\nATGTTT\n', '>seq1 \nATGATG\n>seq2\nCTGATG\n>seq3\nATGTTT\n'] for ali in alignments: t = EvolTree('((seq1,seq2),seq3);') t.link_to_alignment(ali) self.assertEqual((t & 'seq1').nt_sequence, 'ATGATG') self.assertEqual((t & 'seq2').nt_sequence, 'CTGATG') self.assertEqual((t & 'seq3').nt_sequence, 'ATGTTT')
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)
def test_pickling(self): tree = EvolTree (WRKDIR + 'tree.nw') tree.workdir = ETEPATH + '/examples/data/protamine/PRM1/paml/' tree.link_to_alignment (WRKDIR + 'alignments.fasta_ali') tree.link_to_evol_model (WRKDIR + 'paml/M2/M2.out', 'M2.a') out = open('blip.pik', 'w') dump (tree, out) out.close() out = open('blip.pik') tree2 = load (out) out.close() os.remove('blip.pik') self.assertEqual(str(tree2.get_evol_model('M2.a')), str(tree.get_evol_model('M2.a')) )
def test_load_model(self): tree = EvolTree (WRKDIR + 'tree.nw') tree.workdir = 'examples/evol/data/protamine/PRM1/paml/' tree.link_to_evol_model (WRKDIR + 'paml/fb/fb.out', 'fb') 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') self.assertEqual(sorted(tree._models.keys()), sorted(['fb', 'M1', 'M2', 'M7', 'M8'])) self.assertEqual(len (tree.get_evol_model('M2').branches), 194) self.assertEqual(tree.get_evol_model('fb').lnL, -3265.316569) self.assert_('proportions' in str(tree.get_evol_model('M2'))) self.assert_('p2=' in str(tree.get_evol_model('M2'))) self.assert_('proportions' not in str(tree.get_evol_model('fb'))) self.assert_(' #193' in str(tree.get_evol_model('fb')))
T = EvolTree(TREE_PATH) out = False 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()