jhcepas

def print_table(items, header=None, wrap=True, max_col_width=20, wrap_style="wrap", row_line=False, fix_col_width=False):
    ''' Prints a matrix of data as a human readable table. Matrix
    should be a list of lists containing any type of values that can
    be converted into text strings.

    Two different column adjustment methods are supported through
    the *wrap_style* argument:
    
       wrap: it will wrap values to fit max_col_width (by extending cell height)
       cut: it will strip values to max_col_width

jhcepas

import sys
from ete2 import Tree
import random

def get_json(node):
    # Read ETE tag for duplication or speciation events
    if not hasattr(node, 'evoltype'):
        dup = random.sample(['N','Y'], 1)[0]
    elif node.evoltype == "S":
        dup = "N"

jhcepas

#!/usr/bin/python

import sys
from ete2 import PhyloTree, orthoxml
import argparse

__DESCRIPTION__ = """
etree2orthoxml is a python script that extracts evolutionary events
(speciation and duplication) from a newick tree and exports them as an
OrthoXML file.

jhcepas

#!/usr/bin/env python
import sys
from collections import defaultdict
from ete2 import Tree
try:
    t = Tree(sys.argv[1])
except IndexError:
    print >>sys.stderr, 'you need to provide a newick tree file as first argument\n\n'
    print >>sys.stderr, 'Usage: Newick2FastTreeConstraints.py tree.nw > constraints.fa'
    sys.exit(1)

jhcepas

# pp = painter
# node_links = a list of node links
#   a = node a
#   b = node b
#   a_mode, b_mode: mode 0= node to node. mode 1: if node is internal cover also the descendants 
#   bg = background color
#   lw = linewidth 
#   opa = opacity
#   text, fsize, fcolor, ftype = defines text following the curve

jhcepas

from collections import defaultdict
from ete3 import PhyloTree, TreeStyle, SeqMotifFace, TextFace, RectFace

alg = """
>Dme_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEAL--YYASQTDDIKDRREEAH
>Dme_002
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>Cfa_001
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH

jhcepas

from collections import defaultdict
from ete3 import PhyloTree, TreeStyle, SeqMotifFace, TextFace, RectFace, AttrFace

alg = """
>Dme_001
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEAL--YYASQTDDIKDRREEAH
>Dme_002
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>Cfa_001
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH

jhcepas

import re
from ete3 import SeqGroup, Tree
import sys

alg_file = sys.argv[1] # in fasta format
tree_file = sys.argv[2] # in newick format

alg = SeqGroup(alg_file)
for k,v in alg.name2id.items():
    # converts ilegal newick chars from alg names. 

jhcepas

import sys
import itertools
from ete3 import Tree

try:
    t = Tree()
    t.populate(int(sys.argv[1]), random_branches=True)
except ValueError:
    print >>sys.stderr, 'loading', sys.argv[1]
    t = Tree(sys.argv[1])