def showTreeWithPictures(tree = None, alignment=None, branchLengths=True, bootstrapSupport=True, tolabel=None):
print("ShowTreeWithPictures",tree, alignment, branchLengths,bootstrapSupport, tolabel)
if alignment:
t = EvolTree(tree, alignment,alg_format="paml")
t.link_to_alignment(alignment,alg_format="paml")
else:
t = EvolTree(tree)
nsFG = NodeStyle()
nsFG["fgcolor"] = "darkgreen"
nsFG["size"] = 8
for node in t.traverse():
print(node.node_id)
if tolabel:
if str(node.node_id) in tolabel:
node.set_style(nsFG)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = branchLengths
ts.show_branch_support = bootstrapSupport
out = FILE
if branchLengths:
out+="_Len"
if bootstrapSupport:
out+="_Boot"
t.render(out+"_tree.pdf",tree_style=ts)
t.render(out+"_tree.png",tree_style=ts)
if INTERACTIVE:
t.show(tree_style=ts)
def showAlignmentWithTree(unlabelledTreeAsString,alignment):
t = EvolTree(unlabelledTreeAsString, alignment,alg_format="paml")
t.link_to_alignment(alignment, alg_format="paml")
for node in t.traverse():
print(node)
print(node.node_id, node.name)
print(t.write())
#print(t)
t.show() #layout=evol_clean_layout)
def showTreeWithPictures(tree = None, alignment=None, branchLengths=True, bootstrapSupport=True, tolabel=None,showZScores=False,showLogs=False ):
print(PICS)
print("ShowTreeWithPictures",tree, alignment, branchLengths,bootstrapSupport, tolabel,showZScores,showLogs )
if not alignment:
nsFG = NodeStyle()
nsFG["fgcolor"] = "darkgreen"
nsFG["size"] = 8
t = EvolTree(tree)
#todo:label
#
for node in t.traverse():
print(node.node_id)
if tolabel:
if str(node.node_id) in tolabel:
node.set_style(nsFG)
#q'n'd
if (node.name.split("_")[0]+".png" in PICS):
print(node.name.split("_")[0]+".png")
node.add_face(ImgFace(PICDIR+os.sep+node.name.split("_")[0]+".png", height=50), column=1, position="aligned")
#non GRZM identifier
elif (node.name+".png" in PICS):
print(node.name+".png")
node.add_face(ImgFace(PICDIR+os.sep+node.name+".png", height=50), column=1, position="aligned")
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = branchLengths
ts.show_branch_support = bootstrapSupport
out = FILE
if branchLengths:
out+="_Len"
if bootstrapSupport:
out+="_Boot"
if Z:
out+="_Z"
if L:
out+="_L"
t.render(out+"_tree.pdf",tree_style=ts)
t.render(out+"_tree.png",tree_style=ts)
if INTERACTIVE:
t.show(tree_style=ts)
else:
t = EvolTree(tree, alignment,alg_format="paml")
t.link_to_alignment(alignment,alg_format="paml")
#todo label
#todo check treestyle
#ts = TreeStyle()
#ts.show_leaf_name = True
#ts.show_branch_length = branchLength
#ts.show_branch_support = bootstrapSupport
t.show()
def showAlignmentWithTree(unlabelledTreeAsString,alignment):
t = EvolTree(unlabelledTreeAsString, alignment,alg_format="paml")
#print(t)
#t.run_model ('fb.example')
# t.show()
t.link_to_alignment(alignment, alg_format="paml")
for node in t.traverse():
print(node)
print(node.node_id, node.name)
#t.mark_tree([8], marks=["#1"])
#print(t.write())
print(alignment)
#print(t)
t.show() #layout=evol_clean_layout)
def showAlignmentWithTree(tree,alignment):
print(tree)
t = EvolTree(tree, alignment,alg_format="paml")
nsFG = NodeStyle()
nsFG["fgcolor"] = "darkgreen"
nsFG["size"] = 15
#print(t)
#t.run_model ('fb.example')
# t.show()
t.link_to_alignment(alignment, alg_format="paml")
for node in t.traverse():
print(node)
#if (node.name.split("_")[0] in GENES):
# print(node.name, node.node_id)
# if (node.name.split("_")[0] == "GRMZM2G083841"):
# node.add_face(ImgFace("83841.1.png", height=50, width=50), column=1, position="aligned")
# if (node.name.split("_")[0] == "GRMZM2G473001"):
# node.add_face(ImgFace("473001.png", height=50, width=50), column=1, position="aligned")
node.add_face(TextFace(str(node.node_id)),column=0)
#node.add_face(ImgFace("tux.png", height=50), column=1)
# node.set_style(nsFG)
leaves = node.get_leaf_names()
#leaves = [l for l in leaves if l.split("_")[0] in GENES ]
if leaves !=[]:
print(node.name, node.node_id)
#print(node.node_id)
#t.mark_tree([8], marks=["#1"])
#print(t.write())
#print(alignment)
#print(t)
#t.show() #layout=evol_clean_layout)
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
t = fakeUnroot(t)
t.show(tree_style=ts)
t.render("tree.pdf", tree_style=ts)
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.'
from ete2 import EvolTree
from ete2 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."
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'])
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...'
from ete2 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: '
