Anting Xu , Apr 7 2012

to etetoolkit
I am using ete2.1rev492.

For a tree like this(in newick):
((3,4)2,(6,7)5)1;

Preorder traverse should produce:
1, 2, 3, 4, 5, 6, 7

However, the tree.traverse("preorder") method actually produces:
1, 5, 7, 6, 2, 4, 3

I guess it is a bug in the code. Please confirm. Thanks.

t = Tree ('(((a,b),c));')
t.set_outgroup (t & 'a')

gives an error at "down_branch_connector = self.children[0]" line 837
and delete whole tree.

fix: line 828:
++ if len(self.children)!=1:

-- if len(self.children)>1:

This should be only an option set by users. Useful when very large trees are plotted and optimal radius is too large

Modification of tree structure should ALWAYS clear cache

add convert to ultrametric method

When I try to execute this line of code:

print 'TESTING TREE: ', tree.describe()

Please note tree is an apparently valid tree taken from phylomeDBconnector.

This error rises:

Traceback (most recent call last):
File "test_kegg.py", line 88, in
if utils.get_tree_with_all_subnodes_dbg(node1) and utils.get_tree_with_all_subnodes_dbg(node2):
File "/home/viridis/dev/test-eric/utilities.py", line 50, in get_tree_with_all_subnodes_dbg
print 'TESTING TREE: ', tree.describe()
File "/usr/local/lib/python2.7/dist-packages/ete2-2.0rev111-py2.7.egg/ete2/coretype/tree.py", line 470, in describe
max_node, max_dis = get_farthest_leaf()
NameError: global name 'get_farthest_leaf' is not defined

Inside ETE2 I find tree.py and ther the method describe:
def describe(self):
""" Prints general information about this node and its
connections."""
if len(self.get_tree_root().children)==2:
rooting = "Yes"
elif len(self.get_tree_root().children)>2:
rooting = "No"
else:
rooting = "Unknown"
max_node, max_dis = get_farthest_leaf() #MAYBE A self.get_farthest_leaf() would solve the problem?
print "Number of nodes:\t %d" % len(self.get_descendants())
print "Number of leaves:\t %d" % len(self.get_leaves())
print "Rooted:", rooting
print "Max. lenght to root:"
print "The Farthest descendant node is", max_node.name,
"with a branch distance of", max_dist

Add better warning for optional dependencies
Run tests

Improve algorithms to traverse, prune, get_common_ancestor and search_nodes by name

http://packages.python.org/ete2/tutorial/tutorial_phylogeny.html#visualization-of-phylogenetic-trees

When bgcolor or linetypes are changed in the GUI, the whole tree is redrawn, this can be changed to rerender only the necesary parts.

An AttributeError is raised when double-clicking on a node in the treeview component of ete2-2.1rev492.

Traceback (most recent call last):
  File "/usr/local/lib/python2.7/dist-packages/ete2-2.1rev492-py2.7.egg/ete2/treeview/qt4_gui.py", line 764, in mouseDoubleClickEvent
    bg.setPen(QtGui.QPen(QtGui.QColor("red")))
AttributeError: '_NodeItem' object has no attribute 'setPen'

Almost done in 2.1

t.set_outgroup(t.get_age_balanced_outgroup(sp2age_per_phylome[phylome_id]))
File "/soft/general/python-2.6.4/lib/python2.6/site-packages/ete2-2.1rev492-py2.6.egg/ete2/phylo/phylotree.py", line 330, in get_age_balanced_outgroup
out_age_min = min([species2age[sp] for sp in out_species])
ValueError: min() arg is an empty sequence

el dictionario que le paso: ( --- seria sp2age_per_phylome[phylome_id])

{'DROYA': 5,
'CULPI': 5,
'HUMAN': 9,
'CIOIN': 9,
'AEDAE': 5,
'BOMMO': 5,
'NASVI': 5,
'PEDHC': 5,
'DAPPU': 7,
'DROME': 5,
'APIME': 5,
'ANOGA': 5,
'TRICA': 5,
'DROPS': 5,
'DROMO': 5,
'ACYPI': 5,
'CAEEL': 10}

este son los ids. los arboles son del phyloma 16 (pea aphid). puede ser que hay mas en que no funciona.
he mirado algunos de estos, y tiene una estructura rara, llena de ids duplicados

Phy000YGS1_ACYPI
Phy000YIEH_ACYPI
Phy000YO1U_ACYPI
Phy000YPTH_ACYPI
Phy0010AQT_ACYPI
Phy0010BF4_ACYPI
Phy0010BJW_ACYPI
Phy0010C3I_ACYPI

.

node region
face region

check clusterTree examples.

When reading the attached tree in NHX format, I got more leaves with strange name.
t=Tree("final.ph")

It works perfectly by the following commend.
t=Tree("final.ph",format=9)

However, format "9" seems not for NHX according to the following link.
http://packages.python.org/ete2/tutorial/tutorial_trees.html#reading-and-writing-newick-trees

It also seems for NHX according to the following link.
http://packages.python.org/ete2/tutorial/tutorial_phylogeny.html?highlight=nhx
print t.write(features=["sequence"], format=9)

(((seqA[&&NHX:sequence=MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQF

MALTNVSHQFMALTNVSH],seqB[&&NHX:sequence=MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSY

YAYQTDDQKDRREEAHQFMALTNVSH----------]),seqC[&&NHX:sequence=MAEIPDATIQ---ALTNVSHNIA

VQYLSEFGDLNEALNSYYASQTDDQPDRREEAHQFMALTNVSH----------]),seqD[&&NHX:sequence=MAEAPD

ETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAHQ----------FMALTNVSH]);

As reported to the ETE list:

mynode in mytree
True

And I have found a case in which it doesn't work: if mytree has a single node. Is this intended or a bug?

print mynode
--Phy0008JA7_HUMAN
'Phy0008JA7_HUMAN' in mynode # string case
False
mynode & 'Phy0008JA7_HUMAN' in mynode #node case
False
'Phy0008JA7_HUMAN' == mynode.name #work around
True

Sort branches (swap) according to partition size

t.set_outgroup(t.get_age_balanced_outgroup(sp2age_per_phylome[phylome_id]))
File "/soft/general/python-2.6.4/lib/python2.6/site-packages/ete2-2.1rev492-py2.6.egg/ete2/phylo/phylotree.py", line 330, in get_age_balanced_outgroup
out_age_min = min([species2age[sp] for sp in out_species])
ValueError: min() arg is an empty sequence

el dictionario que le paso: ( --- seria sp2age_per_phylome[phylome_id])

{'DROYA': 5,
'CULPI': 5,
'HUMAN': 9,
'CIOIN': 9,
'AEDAE': 5,
'BOMMO': 5,
'NASVI': 5,
'PEDHC': 5,
'DAPPU': 7,
'DROME': 5,
'APIME': 5,
'ANOGA': 5,
'TRICA': 5,
'DROPS': 5,
'DROMO': 5,
'ACYPI': 5,
'CAEEL': 10}

este son los ids. los arboles son del phyloma 16 (pea aphid). puede ser que hay mas en que no funciona.
he mirado algunos de estos, y tiene una estructura rara, llena de ids duplicados

Phy000YGS1_ACYPI
Phy000YIEH_ACYPI
Phy000YO1U_ACYPI
Phy000YPTH_ACYPI
Phy0010AQT_ACYPI
Phy0010BF4_ACYPI
Phy0010BJW_ACYPI
Phy0010C3I_ACYPI

it fails when all nodes to keep are in the same branch of the root node

t = Tree('(((f:1,g:1)d:1,e:1)b:1,c:1);', format=1)

t.prune(["f", "g", "b", "c"]) #by node names

"b" is removed !!

add new format in order to be abble to display info about root.
right now a way to do it is:
tree.write(format=1)[:-1] + '%s:%s;' % (tree.name, tree.dist)

would be nice to just tree.write(format=12) :)

this is usefull in some cases, as when trying to export to dendropy.

• top- and down-branch could be centered, or aligned to left or right
• faces in the same column are always vertically centered. Other positions can be added.