Example #1
0
 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())
Example #3
0
 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)
Example #5
0
                      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)