15 Nov 2010
example of tests for different rates among sites in clades
"""
__author__ = "Francois-Jose Serra"
__email__ = "*****@*****.**"
__licence__ = "GPLv3"
__version__ = "0.0"
from ete_dev import EvolTree
from ete_dev import NodeStyle
tree = EvolTree ("data/S_example/measuring_S_tree.nw")
tree.link_to_alignment ('data/S_example/alignment_S_measuring_evol.fasta')
print tree
print 'Tree and alignment loaded.'
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'):
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.'
"""
15 Nov 2010
simple example to mark a tree and compute branch-site test of positive selection
"""
__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')
print tree
raw_input ('\n tree and alignment loaded\nHit some key, to start computation of branch site models A and A1 on each branch.\n')
print 'running model M0, for comparison with branch-site models...'
tree.run_model('M0')
# each node/leaf has two kind of identifiers node_id and paml_id, to mark nodes we have to specify
# the node_id of the nodes we want to mark, and the kind of mark in this way:
for leaf in tree:
leaf.node_id
print '\n---------\nNow working with leaf ' + leaf.name
"""
15 Nov 2010
simple example to mark a tree and compute branch-site test of positive selection
"""
__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")
print tree
raw_input(
"\n tree and alignment loaded\nHit some key, to start computation of branch site models A and A1 on each branch.\n"
)
print "running model M0, for comparison with branch-site models..."
tree.run_model("M0")
# each node/leaf has two kind of identifiers node_id and paml_id, to mark nodes we have to specify
# the node_id of the nodes we want to mark, and the kind of mark in this way:
for leaf in tree:
layout for CodemlTree
'''
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
try:
tree = EvolTree("(Orangutan,Human,Chimp);")
tree.link_to_alignment("""
>Human
GAC GCA CGG TGG CAC AAC GTA AAA TTA AGA TGT GAA TTG AGA ACT CTG AAA AAA
TTG GGA CTG GTC GGC TTC AAG GCA GTA AGT CAA TTC GTA ATA CGT CGT GCG
>Chimp
CAC GCC CGA TGG CTC AAC GAA AAG TTA AGA TGC GAA TTG AGA ACT CTG AAA AAA
TTG GGA CTG GAC GGC TAC AAG GCA GTA AGT CAG TAC GTT AAA GGT CGT GCG
>Orangutan
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:
#!/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'])
#!/usr/bin/python
"""
15 Nov 2010
simple example to mark a tree and compute branch-site test of positive selection
"""
__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')
print tree
raw_input(
'\n tree and alignment loaded\nHit some key, to start computation of branch site models A and A1 on each branch.\n'
)
print 'running model M0, for comparison with branch-site models...'
tree.run_model('M0')
# each node/leaf has two kind of identifiers node_id and paml_id, to mark nodes we have to specify
# the node_id of the nodes we want to mark, and the kind of mark in this way:
for leaf in tree:
leaf.node_id
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.'
#!/usr/bin/python
"""
15 Nov 2010
first example, load a tree and compute free ratios model,
to find omega value of each branch.
"""
__author__ = "Francois-Jose Serra"
__email__ = "*****@*****.**"
__licence__ = "GPLv3"
__version__ = "0.0"
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
15 Nov 2010
example of computation and display of an ancestral sequence
computed under free'ratio model.
"""
__author__ = "Francois-Jose Serra"
__email__ = "*****@*****.**"
__licence__ = "GPLv3"
__version__ = "0.0"
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"
example of computation and display of an ancestral sequence
computed under free'ratio model.
"""
__author__ = "Francois-Jose Serra"
__email__ = "*****@*****.**"
__licence__ = "GPLv3"
__version__ = "0.0"
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"
if hasattr(node, "collapsed"):
if node.collapsed == 1:
node.img_style["draw_descendants"] = False
if node.is_leaf():
if hasattr(node, "sequence"):
seqface = MySequenceFace(node.sequence,
"nt",
fsize=10,
col_w=11,
interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
try:
tree = EvolTree("(Orangutan,Human,Chimp);")
tree.link_to_alignment("""
>Human
GAC GCA CGG TGG CAC AAC GTA AAA TTA AGA TGT GAA TTG AGA ACT CTG AAA AAA
TTG GGA CTG GTC GGC TTC AAG GCA GTA AGT CAA TTC GTA ATA CGT CGT GCG
>Chimp
CAC GCC CGA TGG CTC AAC GAA AAG TTA AGA TGC GAA TTG AGA ACT CTG AAA AAA
TTG GGA CTG GAC GGC TAC AAG GCA GTA AGT CAG TAC GTT AAA GGT CGT GCG
>Orangutan
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:
"""
15 Nov 2010
example to illustrate use of sites model, displaying and comparison
"""
__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')
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()
#!/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'])
"""
15 Nov 2010
first example, load a tree and compute free ratios model,
to find omega value of each branch.
"""
__author__ = "Francois-Jose Serra"
__email__ = "*****@*****.**"
__licence__ = "GPLv3"
__version__ = "0.0"
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