Jaime Huerta-Cepas jhcepas

Comparative Genomics and Metagenomics

jhcepas / dist_matrix.py

Created October 18, 2017 08:51

calculates cophenetic matrix of a tree

	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])

jhcepas / sort_alg_by_tree.py

Created March 15, 2017 14:48

Sort a fasta alignment by the order of branches in a phylogenetic tree

	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 / ancestral_seq.py

Last active November 18, 2016 10:39

Some tweaks and ideas to render ancestral sequences aligned to leaf-sequences using ETE3. Resulting image not prefect, but good for data exploration.

	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 / plot_mutations.py

Last active August 30, 2019 12:05

given a tree and its associated alignment, plot column changes for each internal branch

	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 / hgt_visualization.py

Created June 10, 2016 12:01

	# 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 / Newick2FastTreeConstraints.py

Last active August 29, 2015 14:23

Converts a tree in newick format into a FastTree-compatible constraint alignment. It allows for multifurcated nodes.

	#!/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 / etree2orthoxml

Last active August 29, 2015 14:21

Newick tree to OrthoXML converter

	#!/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 / Newick2JSON.py

Last active May 6, 2022 19:37

Converts a newick file into JSON format for d3/TreeWidget javascript component

	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 / print_table.py

Last active June 6, 2020 18:20

nice table printing in python

	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