Python Tree.get_ascii方法代码示例

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
def test():

    custom_functions = {"length":length}

    pattern = """
    (
    len{@.children} > 2
    ,
    len{set{{@.name|}}.intersection{set{{"hello"|"bye"}}}} > 0
    ){length{@.name} < 3 or @.name == "pasa"} and @.dist >= 0.5
    ;
    """

    pattern = TreePattern(pattern, format=8)

    print pattern
    tree = Tree("((hello,(1,2,3)kk)pasa:1, NODE);", format=1)
    print tree.get_ascii(attributes=["name", "dist"])
    print "Pattern matches tree?:", pattern.find_match(tree, custom_functions)

    tree = Tree("((hello,(1,2,3)kk)pasa:0.4, NODE);", format=1)
    print tree.get_ascii(attributes=["name", "dist"])
    print "Pattern matches tree?:", pattern.find_match(tree, custom_functions)

    tree = Tree("(hello,(1,2,3)kk)pasa:1;", format=1)
    print tree.get_ascii(attributes=["name", "dist"])
    print "Pattern matches tree?:", pattern.find_match(tree, custom_functions)

    tree = Tree("((bye,(1,2,3)kk)none:1, NODE);", format=1)
    print tree.get_ascii(attributes=["name", "dist"])
    print "Pattern matches tree?:", pattern.find_match(tree, custom_functions)

    tree = Tree("((bye,(1,2,3)kk)y:1, NODE);", format=1)
    print tree.get_ascii(attributes=["name", "dist"])
    print "Pattern matches tree?:", pattern.find_match(tree, custom_functions)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
 def ete_print(self):
     """ Pretty print.
     
         TODO Debug and document better for case USE_ETE3 == False
     """
     if Cfg.USE_ETE3:
         t = EteTree(self.ete_str(), format=1)
         print(t.get_ascii(show_internal=True))
     else:
         return str(self)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
from ete3 import Tree

t = Tree('((((H,K)D,(F,I)G)B,E)A,((L,(N,Q)O)J,(P,S)M)C)X;', format=1)
print t.get_ascii(show_internal=True)

#print rooted_tree

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
    
    else:  # for child
        #### search the parent node by parent_id
        node_cur = root.search_nodes(name=str(parent_id))
        # there should be only one parent node
        if len(node_cur) == 1:
            #### set child with its id
            node_cur = node_cur[0].add_child(name=str(cell_id))  
            #### set duration
            node_cur.add_feature("dist", time_duration)
            
            # set node style
            node_cur.set_style(ns)
            
            # set node name to face
            nameFace = TextFace(node_cur.name)
            nameFace.fgcolor = "white"
            nameFace.fsize = 15
            nameFace.background.color = "green"
            node_cur.add_face(nameFace, column=1, position="branch-bottom")
        else:
            raise RuntimeError("the cell id should be unique!")
            
        
#node = root.search_nodes(name=str(5))
#node[0].add_feature("dist", 1.5)
    
print root.get_ascii()

root.show(tree_style=ts)

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
parser.add_argument(
    '--verbose', action='store_true',
    help=('Print information about the outgroup (if any) taxa to standard '
          'error'))

args = parser.parse_args()

tree = Tree(args.treeFile.read())

if args.outgroupRegex:
    from re import compile
    regex = compile(args.outgroupRegex)
    taxa = [leaf.name for leaf in tree.iter_leaves() if regex.match(leaf.name)]

    if taxa:
        ca = tree.get_common_ancestor(taxa)
        if args.verbose:
            print('Taxa for outgroup:', taxa, file=sys.stderr)
            print('Common ancestor:', ca.name, file=sys.stderr)
            print('Common ancestor is tree:', tree == ca, file=sys.stderr)

        if len(taxa) == 1:
            tree.set_outgroup(tree & taxa[0])
        else:
            if ca == tree:
                tree.set_outgroup(tree.get_midpoint_outgroup())
            else:
                tree.set_outgroup(tree.get_common_ancestor(taxa))

print(tree.get_ascii())

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
def main():
    random.seed()
    #Open the files
    trainingFile = open("data/training.txt","r")
    testFile = open("data/test.txt", "r")
    trainingExamples = []
    testExamples = []
    #Read eaxmaples from files
    for line in trainingFile:
        trainingExamples.append(line.split())
    for line in testFile:
        testExamples.append(line.split())
    #Convert 2 to 0 in examples and make the values integers
    for i in xrange(0, len(trainingExamples)):
        for j in xrange(0, len(trainingExamples[0])):
            if trainingExamples[i][j] == '1':
                trainingExamples[i][j] = 1
            else:
                trainingExamples[i][j] = 0
    for i in xrange(0, len(testExamples)):
        for j in xrange(0, len(testExamples[0])):
            if testExamples[i][j] == '1':
                testExamples[i][j] = 1
            else:
                testExamples[i][j] = 0
    #Create the attrbutes 0 to 6
    attributes = [x for x in range(0, len(trainingExamples[0])-1)]
    #Create deep copy in order for training with random Importance
    random_attributes = copy.deepcopy(attributes)
    #Close files
    trainingFile.close()
    testFile.close()
    #Train two trees, one with regular Importance and one with random Importance
    tree = train(trainingExamples, attributes)
    random_tree = train(trainingExamples, random_attributes, True)
    #Test the trees
    accuracy = test(tree, testExamples)
    random_accuracy = test(random_tree, testExamples)
    print accuracy
    print random_accuracy
    #Visualise the trees
    s = print_tree(tree)
    s = s[:-1]
    s += ';'
    print s

    try:
        t = Tree(s, format=1)
        print t.get_ascii(show_internal=True)
    except NameError as e:
        pass

    r = print_tree(random_tree)
    r = r[:-1]
    r += ';'
    print r

    try:
        rt = Tree(r, format=1)
        print rt.get_ascii(show_internal=True)
    except NameError as e:
        pass

# 需要导入模块: from ete3 import Tree [as 别名]
# 或者: from ete3.Tree import get_ascii [as 别名]
def run(args):
    if args.text_mode:
        from ete3 import Tree
        for tindex, tfile in enumerate(args.src_tree_iterator):
            #print tfile
            if args.raxml:
                nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
                t = Tree(nw)
            else:
                t = Tree(tfile)

            print(t.get_ascii(show_internal=args.show_internal_names,
                              attributes=args.show_attributes))
        return

    import random
    import re
    import colorsys
    from collections import defaultdict
    from ete3 import (Tree, PhyloTree, TextFace, RectFace, faces, TreeStyle,
                         add_face_to_node, random_color)

    global FACES

    if args.face:
        FACES = parse_faces(args.face)
    else:
        FACES = []

    # VISUALIZATION
    ts = TreeStyle()
    ts.mode = args.mode
    ts.show_leaf_name = True
    ts.tree_width = args.tree_width


    for f in FACES:
        if f["value"] == "@name":
            ts.show_leaf_name = False
            break

    if args.as_ncbi:
        ts.show_leaf_name = False
        FACES.extend(parse_faces(
            ['value:@sci_name, size:10, fstyle:italic',
             'value:@taxid, color:grey, size:6, format:" - %s"',
             'value:@sci_name, color:steelblue, size:7, pos:b-top, nodetype:internal',
             'value:@rank, color:indianred, size:6, pos:b-bottom, nodetype:internal',
         ]))


    if args.alg:
        FACES.extend(parse_faces(
            ['value:@sequence, size:10, pos:aligned, ftype:%s' %args.alg_type]
         ))

    if args.heatmap:
        FACES.extend(parse_faces(
            ['value:@name, size:10, pos:aligned, ftype:heatmap']
         ))

    if args.bubbles:
        for bubble in args.bubbles:
            FACES.extend(parse_faces(
                ['value:@%s, pos:float, ftype:bubble, opacity:0.4' %bubble,
             ]))

    ts.branch_vertical_margin = args.branch_separation
    if args.show_support:
        ts.show_branch_support = True
    if args.show_branch_length:
        ts.show_branch_length = True
    if args.force_topology:
        ts.force_topology = True
    ts.layout_fn = lambda x: None

    for tindex, tfile in enumerate(args.src_tree_iterator):
        #print tfile
        if args.raxml:
            nw = re.sub(":(\d+\.\d+)\[(\d+)\]", ":\\1[&&NHX:support=\\2]", open(tfile).read())
            t = PhyloTree(nw)
        else:
            t = PhyloTree(tfile)


        if args.alg:
            t.link_to_alignment(args.alg, alg_format=args.alg_format)

        if args.heatmap:
            DEFAULT_COLOR_SATURATION = 0.3
            BASE_LIGHTNESS = 0.7
            def gradient_color(value, max_value, saturation=0.5, hue=0.1):
                def rgb2hex(rgb):
                    return '#%02x%02x%02x' % rgb
                def hls2hex(h, l, s):
                    return rgb2hex( tuple([int(x*255) for x in colorsys.hls_to_rgb(h, l, s)]))

                lightness = 1 - (value * BASE_LIGHTNESS) / max_value
                return hls2hex(hue, lightness, DEFAULT_COLOR_SATURATION)

#.........这里部分代码省略.........