def __write_algn(self, fullpath):
"""
to write algn in paml format
"""
seq_group = SeqGroup()
for n in self:
seq_group.id2seq[n.node_id] = n.nt_sequence
seq_group.id2name[n.node_id] = n.name
seq_group.name2id[n.name] = n.node_id
seq_group.write(outfile=fullpath, format='paml')
def __write_algn(self, fullpath):
"""
to write algn in paml format
"""
seq_group = SeqGroup ()
for n in self:
seq_group.id2seq [n.node_id] = n.nt_sequence
seq_group.id2name [n.node_id] = n.name
seq_group.name2id [n.name ] = n.node_id
seq_group.write (outfile=fullpath, format='paml')
def link_to_alignment(self, alignment, alg_format="fasta"):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence",alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves)>0:
print >>sys.stderr, \
"Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves)
def link_to_alignment(self, alignment, alg_format="fasta", **kwargs):
missing_leaves = []
missing_internal = []
if type(alignment) == SeqGroup:
alg = alignment
else:
alg = SeqGroup(alignment, format=alg_format, **kwargs)
# sets the seq of
for n in self.traverse():
try:
n.add_feature("sequence",alg.get_seq(n.name))
except KeyError:
if n.is_leaf():
missing_leaves.append(n.name)
else:
missing_internal.append(n.name)
if len(missing_leaves)>0:
print >>sys.stderr, \
"Warnning: [%d] terminal nodes could not be found in the alignment." %\
len(missing_leaves)
from ete_dev import PhyloTree, PhylomeDBConnector, SeqGroup
p = PhylomeDBConnector()
w,x, t = p.get_best_tree("Hsa0000001", 1)
a, l = p.get_clean_alg("Hsa0000001", 1)
A = SeqGroup(a, "iphylip")
for s in A.id2seq:
A.id2seq[s]=A.id2seq[s][:30]
t.link_to_alignment(A)
print t.get_species()
print t
t.set_outgroup(t&"Ddi0002240")
sp = PhyloTree("(((((((((((Hsa, Ptr), Mmu), ((Mms, Rno), (Bta, Cfa))), Mdo), Gga), Xtr), (Dre, Fru))),Cin) (Dme, Aga)), Ddi);")
reconciled, evs = t.reconcile(sp)
print reconciled
reconciled.show()