def testScaleEdgesNoLens(self):
newick_list = [
'(5,((4,3),2),1);', '(5,(4,3,2),1);', '(5,((4,3),2),1);',
'(5,(4,3),2,1);', '(5,((4,3),2),1);', '(5,4,3,2,1);'
]
tree_list = dendropy.TreeList(stream=StringIO("""%s""" %
"\n".join(newick_list)),
schema="newick")
for n, tree in enumerate(tree_list):
treemanip.scale_edges(tree, 2.0)
self.assertEqual(newick_list[n], "%s;" % tree.as_newick_string())
def testScaleEdgesNoLens(self):
newick_list = ['(5,((4,3),2),1);',
'(5,(4,3,2),1);',
'(5,((4,3),2),1);',
'(5,(4,3),2,1);',
'(5,((4,3),2),1);',
'(5,4,3,2,1);']
tree_list = dendropy.TreeList(
stream=StringIO("""%s""" % "\n".join(newick_list)),
schema="newick")
for n, tree in enumerate(tree_list):
treemanip.scale_edges(tree, 2.0)
self.assertEqual(newick_list[n], "%s;" % tree.as_newick_string())
def testScaleEdgesRealTest(self):
newick_list = ['(5:3,((4:1,3:1):1.5,2:3),1:0);',
'(5:7.5,4:1,3:-2,2:4,1:.1);']
doubled = ['(5:6.0,((4:2.0,3:2.0):3.0,2:6.0),1:0.0);',
'(5:15.0,4:2.0,3:-4.0,2:8.0,1:0.2);']
as_f = ['(5:3.0,((4:1.0,3:1.0):1.5,2:3.0),1:0.0);',
'(5:7.5,4:1.0,3:-2.0,2:4.0,1:0.1);']
tree_list = dendropy.TreeList(
stream=StringIO("""%s""" % "\n".join(newick_list)),
schema="newick")
for n, tree in enumerate(tree_list):
treemanip.scale_edges(tree, 2)
self.assertEqual(doubled[n], "%s;" % tree.as_newick_string())
for n, tree in enumerate(tree_list):
treemanip.scale_edges(tree, .5)
self.assertEqual(as_f[n], "%s;" % tree.as_newick_string())
if __name__ == '__main__':
from optparse import OptionParser
parser = OptionParser()
parser.add_option("-m", "--multiplier", dest="multip", default=1.0,
type="float",
help="The multiplier used for every branch length.")
parser.add_option("-n", "--nexus", dest="schema", action="store_const", const="NEXUS", default="NEWICK",
help="Tree is in NEXUS schema.")
(options, args) = parser.parse_args()
if len(args) > 1:
sys.exit("At most one argument (a newick tree string with branch lengths) can be specified")
if len(args) == 1:
s = open(args[0], 'rU')
else:
newick = sys.stdin.read()
s = StringIO.StringIO(newick)
multip = options.multip
d = DataSet()
d.read(s, schema=options.schema, rooted=True)
if len(d.tree_lists) == 0:
sys.exit("No trees found in file.")
for tb in d.tree_lists:
for tree in tb:
scale_edges(tree, multip)
d.write_to_stream(sys.stdout, schema=options.schema)
help="The multiplier used for every branch length.")
parser.add_option("-n",
"--nexus",
dest="schema",
action="store_const",
const="NEXUS",
default="NEWICK",
help="Tree is in NEXUS schema.")
(options, args) = parser.parse_args()
if len(args) > 1:
sys.exit(
"At most one argument (a newick tree string with branch lengths) can be specified"
)
if len(args) == 1:
s = open(args[0], 'rU')
else:
newick = sys.stdin.read()
s = StringIO.StringIO(newick)
multip = options.multip
d = DataSet()
d.read(s, schema=options.schema, rooted=True)
if len(d.tree_lists) == 0:
sys.exit("No trees found in file.")
for tb in d.tree_lists:
for tree in tb:
scale_edges(tree, multip)
d.write_to_stream(sys.stdout, schema=options.schema)