# 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
""" # 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
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)
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()