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from __future__ import absolute_import
from __future__ import print_function
import unittest
from .. import PhyloTree, SeqGroup
from .datasets import *
class Test_phylo_module(unittest.TestCase):
# ALL TESTS USE THIS EXAMPLE TREE
#
# /-Dme_001
# /--------|
# | \-Dme_002
# |
# | /-Cfa_001
# | /--------|
# | | \-Mms_001
# | |
#---------| | /-Hsa_001
# | | /--------|
# | /--------| /--------| \-Hsa_003
# | | | | |
# | | | /--------| \-Ptr_001
# | | | | |
# | | | | \-Mmu_001
# | | \--------|
# \--------| | /-Hsa_004
# | | /--------|
# | \--------| \-Ptr_004
# | |
# | \-Mmu_004
# |
# | /-Ptr_002
# \--------|
# | /-Hsa_002
# \--------|
# \-Mmu_002
def test_link_alignmets(self):
""" Phylotree can be linked to SeqGroup objects"""
fasta = """
>seqA
MAEIPDETIQQFMALT---HNIAVQYLSEFGDLNEALNSYYASQTDDIKDRREEAH
>seqB
MAEIPDATIQQFMALTNVSHNIAVQY--EFGDLNEALNSYYAYQTDDQKDRREEAH
>seqC
MAEIPDATIQ---ALTNVSHNIAVQYLSEFGDLNEALNSYYASQTDDQPDRREEAH
>seqD
MAEAPDETIQQFMALTNVSHNIAVQYLSEFGDLNEAL--------------REEAH
"""
# Caution with iphylip string. blank spaces in the beginning are important
iphylip = """
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
"""
# Loads a tree and link it to an alignment. As usual, 'alignment' can be
# the path to a file or the data themselves in text string format
alg1 = SeqGroup(fasta)
alg2 = SeqGroup(iphylip, format="iphylip")
t = PhyloTree("(((seqA,seqB),seqC),seqD);", alignment=fasta, alg_format="fasta")
for l in t.get_leaves():
self.assertEqual(l.sequence, alg1.get_seq(l.name))
# The associated alignment can be changed at any time
t.link_to_alignment(alignment=alg2, alg_format="iphylip")
for l in t.get_leaves():
self.assertEqual(l.sequence, alg2.get_seq(l.name))
def test_get_sp_overlap_on_all_descendants(self):
""" Tests ortholgy prediction using the sp overlap"""
# Creates a gene phylogeny with several duplication events at
# different levels.
t = PhyloTree('((Dme_001,Dme_002),(((Cfa_001,Mms_001),((((Hsa_001,Hsa_003),Ptr_001),Mmu_001),((Hsa_004,Ptr_004),Mmu_004))),(Ptr_002,(Hsa_002,Mmu_002))));')
# Scans the tree using the species overlap algorithm and detect all
# speciation and duplication events
events = t.get_descendant_evol_events()
# Check that all duplications are detected
dup1 = t.get_common_ancestor("Hsa_001", "Hsa_004")
self.assertEqual(dup1.evoltype, "D")
dup2 = t.get_common_ancestor("Dme_001", "Dme_002")
self.assertEqual(dup2.evoltype, "D")
dup3 = t.get_common_ancestor("Hsa_001", "Hsa_002")
self.assertEqual(dup3.evoltype, "D")
dup4 = t.get_common_ancestor("Hsa_001", "Hsa_003")
self.assertEqual(dup4.evoltype, "D")
# All other nodes should be speciation
for node in t.traverse():
if not node.is_leaf() and \
node not in set([dup1, dup2, dup3, dup4]):
self.assertEqual(node.evoltype, "S")
# Check events
for e in events:
self.assertEqual(e.node.evoltype, e.etype)
# Check orthology/paralogy prediction
orthologs = set()
for e in events:
if e.node == dup1:
self.assertEqual(e.inparalogs, set(['Ptr_001', 'Hsa_001', 'Mmu_001', 'Hsa_003']))
self.assertEqual(e.outparalogs, set(['Mmu_004', 'Ptr_004', 'Hsa_004']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.outparalogs, e.out_seqs)
self.assertEqual(e.inparalogs, e.in_seqs)
elif e.node == dup2:
self.assertEqual(e.inparalogs, set(['Dme_001']))
self.assertEqual(e.outparalogs, set(['Dme_002']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.outparalogs, e.out_seqs)
self.assertEqual(e.inparalogs, e.in_seqs)
elif e.node == dup3:
self.assertEqual(e.inparalogs, set(['Hsa_003', 'Cfa_001', 'Ptr_001', 'Hsa_001', 'Ptr_004', 'Hsa_004', 'Mmu_004', 'Mmu_001', 'Mms_001']))
self.assertEqual(e.outparalogs, set(['Hsa_002', 'Ptr_002', 'Mmu_002']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.outparalogs, e.out_seqs)
self.assertEqual(e.inparalogs, e.in_seqs)
elif e.node == dup4:
self.assertEqual(e.inparalogs, set(['Hsa_001']))
self.assertEqual(e.outparalogs, set(['Hsa_003']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.outparalogs, e.out_seqs)
self.assertEqual(e.inparalogs, e.in_seqs)
else:
key1 = list(e.inparalogs)
key2 = list(e.orthologs)
key1.sort()
key2.sort()
orthologs.add(tuple(sorted([tuple(key1), tuple(key2)])))
orthologies = [
[set(['Dme_001', 'Dme_002']), set(['Ptr_001', 'Cfa_001', 'Hsa_002', 'Hsa_003', 'Ptr_002', 'Hsa_001', 'Ptr_004', 'Hsa_004', 'Mmu_004', 'Mmu_001', 'Mms_001', 'Mmu_002'])],
[set(['Mms_001', 'Cfa_001']), set(['Hsa_003', 'Ptr_001', 'Hsa_001', 'Ptr_004', 'Hsa_004', 'Mmu_004', 'Mmu_001'])],
[set(['Ptr_002']), set(['Hsa_002', 'Mmu_002'])],
[set(['Cfa_001']), set(['Mms_001'])],
[set(['Hsa_002']), set(['Mmu_002'])],
[set(['Hsa_003', 'Hsa_001', 'Ptr_001']), set(['Mmu_001'])],
[set(['Ptr_004', 'Hsa_004']), set(['Mmu_004'])],
[set(['Hsa_003', 'Hsa_001']), set(['Ptr_001'])],
[set(['Hsa_004']), set(['Ptr_004'])]
]
expected_orthologs = set()
for l1,l2 in orthologies:
key1 = list(l1)
key2 = list(l2)
key1.sort()
key2.sort()
expected_orthologs.add(tuple(sorted([tuple(key1), tuple(key2)])))
# Are all orthologies as expected
self.assertEqual(expected_orthologs, orthologs)
# Test different sos_thr
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = t.get_descendant_evol_events(0.1)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'D')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'D')
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = t.get_descendant_evol_events(0.5)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'S')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'D')
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = seed.get_my_evol_events(0.75)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'S')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'S')
def test_get_sp_overlap_on_a_seed(self):
""" Tests ortholgy prediction using sp overlap"""
# Creates a gene phylogeny with several duplication events at
# different levels.
t = PhyloTree('((Dme_001,Dme_002),(((Cfa_001,Mms_001),((((Hsa_001,Hsa_003),Ptr_001),Mmu_001),((Hsa_004,Ptr_004),Mmu_004))),(Ptr_002,(Hsa_002,Mmu_002))));')
# Scans the tree using the species overlap algorithm
seed = t.search_nodes(name="Hsa_001")[0]
events = seed.get_my_evol_events()
# Check that duplications are detected
dup1 = t.get_common_ancestor("Hsa_001", "Hsa_004")
#print(dup1)
self.assertEqual(dup1.evoltype, "D")
# This duplication is not in the seed path
dup2 = t.get_common_ancestor("Dme_001", "Dme_002")
self.assertTrue(not hasattr(dup2, "evoltype"))
dup3 = t.get_common_ancestor("Hsa_001", "Hsa_002")
self.assertEqual(dup3.evoltype, "D")
dup4 = t.get_common_ancestor("Hsa_001", "Hsa_003")
self.assertEqual(dup4.evoltype, "D")
# All other nodes should be speciation
node = seed
while node:
if not node.is_leaf() and \
node not in set([dup1, dup2, dup3, dup4]):
self.assertEqual(node.evoltype, "S")
node = node.up
# Check events
for e in events:
self.assertEqual(e.node.evoltype, e.etype)
# Check orthology/paralogy prediction
orthologs = set()
for e in events:
if e.node == dup1:
self.assertEqual(e.inparalogs, set(['Hsa_001', 'Hsa_003']))
self.assertEqual(e.outparalogs, set(['Hsa_004']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.in_seqs, set(['Ptr_001', 'Hsa_001', 'Mmu_001', 'Hsa_003']))
self.assertEqual(e.out_seqs, set(['Mmu_004', 'Ptr_004', 'Hsa_004']))
elif e.node == dup3:
self.assertEqual(e.inparalogs, set(['Hsa_003', 'Hsa_001', 'Hsa_004' ]))
self.assertEqual(e.outparalogs, set(['Hsa_002']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.in_seqs, set(['Hsa_003', 'Cfa_001', 'Ptr_001', 'Hsa_001', 'Ptr_004', 'Hsa_004', 'Mmu_004', 'Mmu_001', 'Mms_001']))
self.assertEqual(e.out_seqs, set(['Hsa_002', 'Ptr_002', 'Mmu_002']))
elif e.node == dup4:
self.assertEqual(e.inparalogs, set(['Hsa_001']))
self.assertEqual(e.outparalogs, set(['Hsa_003']))
self.assertEqual(e.orthologs, set())
self.assertEqual(e.in_seqs, set(['Hsa_001']))
self.assertEqual(e.out_seqs, set(['Hsa_003']))
else:
key1 = list(e.inparalogs)
key2 = list(e.orthologs)
key1.sort()
key2.sort()
orthologs.add(tuple(sorted([tuple(key1), tuple(key2)])))
orthologies = [
[set(['Dme_001', 'Dme_002']), set([ 'Hsa_002', 'Hsa_003', 'Hsa_001', 'Hsa_004' ])],
[set(['Mms_001', 'Cfa_001']), set(['Hsa_003', 'Hsa_001', 'Hsa_004'])],
[set(['Hsa_003', 'Hsa_001']), set(['Mmu_001'])],
[set(['Hsa_003', 'Hsa_001']), set(['Ptr_001'])],
]
expected_orthologs = set()
for l1,l2 in orthologies:
key1 = list(l1)
key2 = list(l2)
key1.sort()
key2.sort()
expected_orthologs.add(tuple(sorted([tuple(key1), tuple(key2)])))
# Are all orthologies as expected
self.assertEqual(expected_orthologs, orthologs)
# Test different sos_thr
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = seed.get_my_evol_events(0.1)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'D')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'D')
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = seed.get_my_evol_events(0.50)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'S')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'D')
t = PhyloTree('(((SP1_a, SP2_a), (SP3_a, SP1_b)), (SP1_c, SP2_c));')
seed = (t & 'SP1_a')
events = seed.get_my_evol_events(0.75)
self.assertEqual(t.get_common_ancestor(seed, 'SP3_a').evoltype, 'S')
self.assertEqual(t.get_common_ancestor(seed, 'SP1_c').evoltype, 'S')
def test_reconciliation(self):
""" Tests ortholgy prediction based on the species reconciliation method"""
gene_tree_nw = '((Dme_001,Dme_002),(((Cfa_001,Mms_001),((Hsa_001,Ptr_001),Mmu_001)),(Ptr_002,(Hsa_002,Mmu_002))));'
species_tree_nw = "((((Hsa, Ptr), Mmu), (Mms, Cfa)), Dme);"
genetree = PhyloTree(gene_tree_nw)
sptree = PhyloTree(species_tree_nw)
recon_tree, events = genetree.reconcile(sptree)
# Check that reconcilied tree nodes have the correct lables:
# gene loss, duplication, etc.
expected_recon = "((Dme_001:1,Dme_002:1)1:1[&&NHX:evoltype=D],(((Cfa_001:1,Mms_001:1)1:1[&&NHX:evoltype=S],((Hsa_001:1,Ptr_001:1)1:1[&&NHX:evoltype=S],Mmu_001:1)1:1[&&NHX:evoltype=S])1:1[&&NHX:evoltype=S],((Mms:1[&&NHX:evoltype=L],Cfa:1[&&NHX:evoltype=L])1:1[&&NHX:evoltype=L],(((Hsa:1[&&NHX:evoltype=L],Ptr_002:1)1:1[&&NHX:evoltype=L],Mmu:1[&&NHX:evoltype=L])1:1[&&NHX:evoltype=L],((Ptr:1[&&NHX:evoltype=L],Hsa_002:1)1:1[&&NHX:evoltype=L],Mmu_002:1)1:1[&&NHX:evoltype=S])1:1[&&NHX:evoltype=D])1:1[&&NHX:evoltype=L])1:1[&&NHX:evoltype=D])[&&NHX:evoltype=S];"
self.assertEqual(recon_tree.write(["evoltype"], format=9), PhyloTree(expected_recon).write(features=["evoltype"],format=9))
def test_miscelaneus(self):
""" Test several things """
# Creates a gene phylogeny with several duplication events at
# different levels.
t = PhyloTree('((Dme_001,Dme_002),(((Cfa_001,Mms_001),((((Hsa_001,Hsa_003),Ptr_001),Mmu_001),((Hsa_004,Ptr_004),Mmu_004))),(Ptr_002,(Hsa_002,Mmu_002))));')
# Create a dictionary with relative ages for the species present in
# the phylogenetic tree. Note that ages are only relative numbers to
# define which species are older, and that different species can
# belong to the same age.
sp2age = {
'Hsa': 1, # Homo sapiens (Hominids)
'Ptr': 2, # P. troglodytes (primates)
'Mmu': 2, # Macaca mulata (primates)
'Mms': 3, # Mus musculus (mammals)
'Cfa': 3, # Canis familiaris (mammals)
'Dme': 4 # Drosophila melanogaster (metazoa)
}
# Check that dup ages are correct
dup1 = t.get_common_ancestor("Hsa_001", "Hsa_004")
self.assertEqual(dup1.get_age(sp2age), 2)
dup2 = t.get_common_ancestor("Dme_001", "Dme_002")
self.assertEqual(dup2.get_age(sp2age), 4)
dup3 = t.get_common_ancestor("Hsa_001", "Hsa_002")
self.assertEqual(dup3.get_age(sp2age), 3)
dup4 = t.get_common_ancestor("Hsa_001", "Hsa_003")
self.assertEqual(dup4.get_age(sp2age), 1)
# Check rooting options
expected_root = t.search_nodes(name="Dme_002")[0]
expected_root.dist += 2.3
self.assertEqual(t.get_farthest_oldest_leaf(sp2age), expected_root)
#print t
#print t.get_farthest_oldest_node(sp2age)
# Check get species functions
self.assertEqual(t.get_species(), set(sp2age.keys()))
self.assertEqual(set([sp for sp in t.iter_species()]), set(sp2age.keys()))
def test_colappse(self):
t = PhyloTree('((Dme_001,Dme_002),(((Cfa_001,Mms_001),((((Hsa_001,Hsa_001),Ptr_001),Mmu_001),((Hsa_004,Ptr_004),Mmu_004))),(Ptr_002,(Hsa_002,Mmu_002))));')
collapsed_hsa = '((Dme_001:1,Dme_002:1)1:1,(((Cfa_001:1,Mms_001:1)1:1,(((Ptr_001:1,Hsa_001:1)1:1,Mmu_001:1)1:1,((Hsa_004:1,Ptr_004:1)1:1,Mmu_004:1)1:1)1:1)1:1,(Ptr_002:1,(Hsa_002:1,Mmu_002:1)1:1)1:1)1:1);'
t2 = t.collapse_lineage_specific_expansions(['Hsa'])
self.assertEqual(str(collapsed_hsa), str(t2.write()))
with self.assertRaises(TypeError):
print(t.collapse_lineage_specific_expansions('Hsa'))
if __name__ == '__main__':
unittest.main()
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