#
# t.show(tree_style=ts)
for node in t: #.iter_search_nodes():
# name = node.name
# name = name[name.find("_")+1:]
# node.name = name
print node.name
if node.name == "41":
node.dist = 5e-05
# t.write(outfile='/Volumes/MP_HD/CI_GENOME_SEQ/CI_gene_coverage (generate stat for sig diff cov)/gene_copy_no_tree/CI_node_assignments_tree_nos.nwk',format=1,)
ts = TreeStyle()
t.show(tree_style=ts)
#
# print infile
#
# def rem_names(s):
# if "_" in s:
# p = s.find("_")
# nstr = s[:p-3]+s[p+1:]
# return rem_names(nstr)
# else:
# return s
#
# def rem_supports(s):
# if ":" in s:
# p = s.find(":")
>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)
# Show very large algs
tree = PhyloTree('(Orangutan,Human,Chimp);')
tree.link_to_alignment(">Human\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Chimp\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]) + \
"\n>Orangutan\n" + ''.join([_aabgcolors.keys()[int(random() * len (_aabgcolors))] for _ in xrange (5000)]))
tree.dist = 0
ts = TreeStyle()
ts.title.add_face(TextFace("better not set interactivity if alg is very large", fsize=15), column=0)
ts.layout_fn = test_layout_phylo_aa
tree.show(tree_style=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")
# | /-Cfa_001 # | /--------| # | | \-Mms_001 #---------| /--------| # | | | /-Hsa_001 # | | | /--------| # | | \--------| \-Ptr_001 # | | | # | | \-Mmu_001 # \--------| # | /-Mms # | /--------| # | | \-Cfa # | | # | | /-Hsa # \--------| /--------| # | /--------| \-Ptr_002 # | | | # | | \-Mmu # \--------| # | /-Ptr # | /--------| # \--------| \-Hsa_002 # | # \-Mmu_002 # # And we can visualize the trees using the default phylogeny # visualization layout genetree.show() recon_tree.show()
