def load_tree_sequences(nwk_file, fasta_file):
'''
Load a tree with associated sequences on leaves.
'''
tree = PhyloTree(newick=nwk_file, format=1)
tree.link_to_alignment(alignment=fasta_file, alg_format='fasta')
return tree
def load_tree(f_tree, f_align):
# Tree style
ts = TreeStyle()
ts.show_leaf_name = True
ts.show_branch_length = True
ts.show_branch_support = True
ts.branch_vertical_margin = 10
# Load phylogenetic tree
tree = PhyloTree(f_tree.read())
if f_align is not None:
tree.link_to_alignment(f_align.read())
return tree, ts
from Bio import SeqIO
from Bio import motifs
from Bio.Cluster import distancematrix
from Bio.Cluster import clustercentroids
records = list(SeqIO.parse("./txt/cm_perm_sequence_27_social.fasta", "fasta"))
for seq_record in SeqIO.parse("./txt/cm_perm_sequence_27_social.fasta", "fasta"):
print seq_record.id
print repr(seq_record.seq)
print len(seq_record)
from Bio.Align.Applications import ClustalwCommandline
clustalx = '/Applications/PhylogeneticAnalysis/clustalw2'
cline = ClustalwCommandline(clustalx, infile="./txt/cm_perm_sequence_27_social.fasta")
print cline
stdout, stderr = cline()
from Bio import Phylo
tree = Phylo.read("./txt/cm_perm_sequence_27_social.dnd", "newick")
tree.rooted = True
#Phylo.draw(tree)
from ete2 import Tree
from ete2 import PhyloTree
t = PhyloTree('./txt/cm_perm_sequence_27_social.dnd')
t.link_to_alignment(alignment="./txt/cm_perm_sequence_27_social.fasta", alg_format="fasta")
#from ete2 import ClusterTree
#t = ClusterTree('./txt/cm_perm_sequence_27_social.dnd')
t.show()
#t.show("heatmap")
#t.show("cluster_cbars")
#t.show("cluster_bars")
#t.show("cluster_lines")
if node.collapsed == 1:
node.img_style["draw_descendants"]= False
if node.is_leaf():
if hasattr (node, "sequence"):
seqface = MySequenceFace(node.sequence, "nt",
fsize=10,
col_w=11, interactive=True)
faces.add_face_to_node(seqface, node, 1, aligned=True)
if __name__ == "__main__":
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment("""
>Chimp
HARWLNEKLRCELRTLKKLGLDGYKAVSQYVKGRA
>Orangutan
DARWINEKLRCVSRTLKKLGLDGYKGVSQYVKGRP
>Human
DARWHNVKLRCELRTLKKLGLVGFKAVSQFVIRRA
""")
nt_sequences = {"Human" : "GACGCACGGTGGCACAACGTAAAATTAAGATGTGAATTGAGAACTCTGAAAAAATTGGGACTGGTCGGCTTCAAGGCAGTAAGTCAATTCGTAATACGTCGTGCG",
"Chimp" : "CACGCCCGATGGCTCAACGAAAAGTTAAGATGCGAATTGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGCAGTAAGTCAGTACGTTAAAGGTCGTGCG",
"Orangutan": "GATGCACGCTGGATCAACGAAAAGTTAAGATGCGTATCGAGAACTCTGAAAAAATTGGGACTGGACGGCTACAAGGGAGTAAGTCAATACGTTAAAGGTCGTCCG"
}
for l in nt_sequences:
(tree & l).nt_sequence = nt_sequences[l]
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("Example for nucleotides...", fsize=15), column=0)
ts.layout_fn = test_layout_evol
tree.show(tree_style=ts)
"""
# Load a tree and link it to an alignment. As usual, 'alignment' can
# be the path to a file or data in text format.
t = PhyloTree("(((seqA,seqB),seqC),seqD);", alignment=fasta_txt, alg_format="fasta")
#We can now access the sequence of every leaf node
print "These are the nodes and its sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
#
# The associated alignment can be changed at any time
t.link_to_alignment(alignment=iphylip_txt, alg_format="iphylip")
# Let's check that sequences have changed
print "These are the nodes and its re-linked sequences:"
for leaf in t.iter_leaves():
print leaf.name, leaf.sequence
#seqD MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAHQ----------FMALTNVSH
#seqC MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAHQFMALTNVSH----------
#seqA MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQFMALTNVSHQFMALTNVSH
#seqB MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAHQFMALTNVSH----------
#
# The sequence attribute is considered as node feature, so you can
# even include sequences in your extended newick format!
print t.write(features=["sequence"], format=9)
#
#
# (((seqA[&&NHX:sequence=MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQF
