def tree_iterator(fname, restrict_species=None, start_line=None, end_line=None):
for ln, line in enumerate(open(fname)):
if start_line is not None and ln < start_line:
continue
elif end_line is not None and ln >= end_line:
break
if line.startswith("#") or not line.strip(): continue
treeid, newick = line.split("\t")
t = PhyloTree(newick, sp_naming_function=extract_species)
if restrict_species:
t.prune([n for n in t.iter_leaves() if n.species in restrict_species])
n2content = t.get_cached_content()
if len(n2content[t]) < 2:
continue
yield treeid, t, n2content
def tree_iterator(fname,
restrict_species=None,
start_line=None,
end_line=None):
for ln, line in enumerate(open(fname)):
if start_line is not None and ln < start_line:
continue
elif end_line is not None and ln >= end_line:
break
if line.startswith("#") or not line.strip(): continue
treeid, newick = line.split("\t")
t = PhyloTree(newick, sp_naming_function=extract_species)
if restrict_species:
t.prune(
[n for n in t.iter_leaves() if n.species in restrict_species])
n2content = t.get_cached_content()
if len(n2content[t]) < 2:
continue
yield treeid, t, n2content
