# # 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()