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()