Python read_tree示例

示例#1

文件： view_mammals.py 项目： mdrasmus/summon

#!/usr/bin/env python-i
# a phylogenetic tree of mammal species
#


print """
NOTE: use Ctrl+right drag and Shift+right drag to zoom the 
      x- and y-axis independently
"""

# import necessary libraries
from summon import sumtree, treelib

# read tree in newick format
tree = treelib.read_tree("mammals.tree")

# draw tree
vis = sumtree.SumTree(tree, name="dog and human gene tree", xscale=40, 
                      winsize=(600, 400))
vis.show()

示例#2

文件： view_olfactory-genes.py 项目： mdrasmus/summon

#!/usr/bin/env python-i
# large phylogeny of mammalian olfactory genes
#


print """
NOTE: use Ctrl+right drag and Shift+right drag to zoom the 
      x- and y-axis independently
"""

# import necessary libraries
from summon import sumtree, util, treelib

# read tree in newick format
tree = treelib.read_tree("olfactory-genes.tree")

# read colormap
colormap = treelib.read_tree_color_map("ensembl.colormap")

# draw tree
vis = sumtree.SumTree(tree, name="dog and human gene tree", xscale=0, 
                      colormap=colormap)
vis.show()