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.'
raw_input ('Tree will be mark in order to contrast Gorilla and Chimpanzee as foreground \nspecies.') marks = ['1', 3, '7'] tree.mark_tree (marks, ['#1'] * 3) print tree.write () # display marked branches in orange for node in tree.traverse (): if not hasattr (node, 'mark'): continue if node.mark == '': continue node.img_style = NodeStyle() node.img_style ['bgcolor'] = '#ffaa00' tree.show() print '''now running branch-site models C and D that represents the addition of one class of sites in on specific branch. These models must be compared to null models M1 and M3. if branch-site models are detected to be significantly better, than, one class of site is evolving at different rate in the marked clade. ''' # TODO: re-enable model M3 print 'running branch-site C...' tree.run_model ('bsC.137') #print 'running branch-site D...'
06 Feb 2011 use slr to compute evolutionary rates """ __author__ = "Francois-Jose Serra" __email__ = "*****@*****.**" __licence__ = "GPLv3" __version__ = "0.0" from ete_dev import EvolTree tree = EvolTree ("data/S_example/measuring_S_tree.nw") tree.link_to_alignment ("data/S_example/alignment_S_measuring_evol.fasta") tree.run_model ('SLR') slr = tree.get_evol_model ('SLR') slr.set_histface (up=False, kind='curve',errors=True, hlines = [1.0,0.3], hlines_col=['black','grey']) tree.show (histfaces=['SLR'])
GAT GCA CGC TGG ATC AAC GAA AAG TTA AGA TGC GTA TCG AGA ACT CTG AAA AAA TTG GGA CTG GAC GGC TAC AAG GGA GTA AGT CAA TAC GTT AAA GGT CGT CCG """) #try: # tree.run_model("fb") # tree.run_model("M2") #except: # pass tree.dist = 0 ts = TreeStyle() ts.title.add_face(TextFace("Example for EvolTree, interactivity shows codons", fsize=15), column=0) ts.layout_fn = test_layout_evol #try: # tree.show(tree_style=ts, histfaces=["M2"]) #except: tree.show(tree_style=ts) except: tree = PhyloTree('(Orangutan,Human,Chimp);') tree.link_to_alignment(""" >Chimp HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA >Orangutan DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP >Human DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA """) nt_sequences = {"Human" : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG", "Chimp" : "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG", "Orangutan": "GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG" } for l in nt_sequences:
from ete_dev import EvolTree tree = EvolTree("data/S_example/measuring_S_tree.nw") print tree raw_input('\n tree loaded, hit some key.\n') print 'Now, it is necessary to link this tree to an alignment:' tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta') raw_input('\n alignment loaded, hit some key to see.\n') tree.show() print ''' we will run free-ratio model that is one of models available through function run_model: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ''' print tree.run_model.__doc__ + '\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++' tree.run_model('fb.example') raw_input('free-ratio model runned, all results are store in a Model object.') fb = tree.get_evol_model('fb.example') print 'Have a look to the parameters used to run this model on codeml: '
from ete_dev import TreeStyle from ete_dev import EvolTree from ete_dev import faces tree = EvolTree("data/S_example/measuring_S_tree.nw") tree.link_to_alignment('data/S_example/alignment_S_measuring_evol.fasta') print tree print '\n Running free-ratio model with calculation of ancestral sequences...' tree.run_model('fb_anc') #tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc') I = TreeStyle() I.force_topology = False I.draw_aligned_faces_as_table = True I.draw_guiding_lines = True I.guiding_lines_type = 2 I.guiding_lines_color = "#CCCCCC" for n in sorted(tree.get_descendants() + [tree], key=lambda x: x.node_id): if n.is_leaf(): continue anc_face = faces.SequenceFace(n.sequence, 'aa', fsize=10, bg_colors={}) I.aligned_foot.add_face(anc_face, 1) I.aligned_foot.add_face( faces.TextFace('node_id: #%d ' % (n.node_id), fsize=8), 0) print 'display result of bs_anc model, with ancestral amino acid sequences.' tree.show(tree_style=I) print '\nThe End.'
from ete_dev import faces tree = EvolTree ("data/S_example/measuring_S_tree.nw") tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta') print tree print '\n Running free-ratio model with calculation of ancestral sequences...' tree.run_model ('fb_anc') #tree.link_to_evol_model('/tmp/ete2-codeml/fb_anc/out', 'fb_anc') I = TreeStyle() I.force_topology = False I.draw_aligned_faces_as_table = True I.draw_guiding_lines = True I.guiding_lines_type = 2 I.guiding_lines_color = "#CCCCCC" for n in sorted (tree.get_descendants()+[tree], key=lambda x: x.node_id): if n.is_leaf(): continue anc_face = faces.SequenceFace (n.sequence, 'aa', fsize=10, bg_colors={}) I.aligned_foot.add_face(anc_face, 1) I.aligned_foot.add_face(faces.TextFace('node_id: #%d '%(n.node_id), fsize=8), 0) print 'display result of bs_anc model, with ancestral amino acid sequences.' tree.show(tree_style=I) print '\nThe End.'
""") #try: # tree.run_model("fb") # tree.run_model("M2") #except: # pass tree.dist = 0 ts = TreeStyle() ts.title.add_face(TextFace( "Example for EvolTree, interactivity shows codons", fsize=15), column=0) ts.layout_fn = test_layout_evol #try: # tree.show(tree_style=ts, histfaces=["M2"]) #except: tree.show(tree_style=ts) except: tree = PhyloTree('(Orangutan,Human,Chimp);') tree.link_to_alignment(""" >Chimp HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA >Orangutan DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP >Human DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA """) nt_sequences = { "Human": "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG", "Chimp": "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
print tree raw_input ('\n tree and alignment loaded\n Hit some key, to start computation of site models M1 and M2.\n') print 'running model M1' tree.run_model ('M1') print 'running model M2' tree.run_model ('M2') print '\n\n comparison of models M1 and M2, p-value: ' + str(tree.get_most_likely ('M2','M1')) #tree.show() print 'by default the hist represented is this one:' tree.show (histfaces=['M2']) print 'but we can choose between many others...' model2 = tree.get_evol_model ('M2') col2 = {'NS' : 'black', 'RX' : 'black', 'RX+': 'black', 'CN' : 'black', 'CN+': 'black', 'PS' : 'black', 'PS+': 'black'} model2.set_histface (up=False, kind='curve', colors=col2, ylim=[0,4], hlines = [2.5, 1.0, 4.0, 0.5], header = 'Many lines, error boxes, background black', hlines_col=['orange', 'yellow', 'red', 'cyan'], errors=True) tree.show(histfaces=['M2'])
#!/usr/bin/python """ 06 Feb 2011 use slr to compute evolutionary rates """ __author__ = "Francois-Jose Serra" __email__ = "*****@*****.**" __licence__ = "GPLv3" __version__ = "0.0" from ete_dev import EvolTree tree = EvolTree("data/S_example/measuring_S_tree.nw") tree.link_to_alignment("data/S_example/alignment_S_measuring_evol.fasta") tree.run_model('SLR') slr = tree.get_evol_model('SLR') slr.set_histface(up=False, kind='curve', errors=True, hlines=[1.0, 0.3], hlines_col=['black', 'grey']) tree.show(histfaces=['SLR'])
from ete_dev import EvolTree tree = EvolTree ("data/S_example/measuring_S_tree.nw") print tree raw_input ('\n tree loaded, hit some key.\n') print 'Now, it is necessary to link this tree to an alignment:' tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta') raw_input ('\n alignment loaded, hit some key to see.\n') tree.show() print ''' we will run free-ratio model that is one of models available through function run_model: +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ ''' print tree.run_model.__doc__ +'\n+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++' tree.run_model ('fb.example') raw_input ('free-ratio model runned, all results are store in a Model object.') fb = tree.get_evol_model('fb.example') print 'Have a look to the parameters used to run this model on codeml: '