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from ete3 import PhyloTree
fasta_txt = """
>seqA
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>seqB
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>seqC
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>seqD
MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
"""
iphylip_txt = """
4 76
seqA MAEIPDETIQ QFMALT---H NIAVQYLSEF GDLNEALNSY YASQTDDIKD RREEAHQFMA
seqB MAEIPDATIQ QFMALTNVSH NIAVQY--EF GDLNEALNSY YAYQTDDQKD RREEAHQFMA
seqC MAEIPDATIQ ---ALTNVSH NIAVQYLSEF GDLNEALNSY YASQTDDQPD RREEAHQFMA
seqD MAEAPDETIQ QFMALTNVSH NIAVQYLSEF GDLNEAL--- ---------- -REEAHQ---
LTNVSHQFMA LTNVSH
LTNVSH---- ------
LTNVSH---- ------
-------FMA LTNVSH
"""
# 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
# MALTNVSHQFMALTNVSH],seqB[&&NHX:sequence=MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSY
# YAYQTDDQKDRREEAHQFMALTNVSH----------]),seqC[&&NHX:sequence=MAEIPDATIQ---ALTNVSHNIA
# VQYLSEFGDLNEALNSYYASQTDDQPDRREEAHQFMALTNVSH----------]),seqD[&&NHX:sequence=MAEAPD
# ETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAHQ----------FMALTNVSH]);
#
# And yes, you can save this newick text and reload it into a PhyloTree instance.
sametree = PhyloTree(t.write(features=["sequence"]))
print "Recovered tree with sequence features:"
print sametree
#
# /-seqA
# /--------|
# /--------| \-seqB
# | |
#---------| \-seqC
# |
# \-seqD
#
print "seqA sequence:", (t&"seqA").sequence
# MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAHQFMALTNVSHQFMALTNVSH
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