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
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'):
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:
