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)
