1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
|
#########################################################################
# MacSyFinder - Detection of macromolecular systems in protein dataset #
# using systems modelling and similarity search. #
# Authors: Sophie Abby, Bertrand Neron #
# Copyright (c) 2014-2024 Institut Pasteur (Paris) and CNRS. #
# See the COPYRIGHT file for details #
# #
# This file is part of MacSyFinder package. #
# #
# MacSyFinder is free software: you can redistribute it and/or modify #
# it under the terms of the GNU General Public License as published by #
# the Free Software Foundation, either version 3 of the License, or #
# (at your option) any later version. #
# #
# MacSyFinder is distributed in the hope that it will be useful, #
# but WITHOUT ANY WARRANTY; without even the implied warranty of #
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
# GNU General Public License for more details . #
# #
# You should have received a copy of the GNU General Public License #
# along with MacSyFinder (COPYING). #
# If not, see <https://www.gnu.org/licenses/>. #
#########################################################################
import os
import shutil
import tempfile
import argparse
from macsypy.gene import Exchangeable
from macsypy.gene import CoreGene, ModelGene
from macsypy.model import Model
from macsypy.profile import ProfileFactory
from macsypy.config import Config, MacsyDefaults
from macsypy.registries import ModelLocation
from macsypy.error import MacsypyError
from tests import MacsyTest
class TestExchangeable(MacsyTest):
def setUp(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 30
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
def tearDown(self):
try:
shutil.rmtree(self.cfg.working_dir)
except Exception:
pass
def test_alternate_of(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
gene_ref.add_exchangeable(homolog_1)
self.assertEqual(homolog_1.alternate_of(), gene_ref)
def test_is_exchangeable(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
self.assertTrue(homolog_1.is_exchangeable)
def test_add_exchangeable(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
homolog_2 = Exchangeable(c_gene, gene_ref)
with self.assertRaises(MacsypyError) as ctx:
homolog_1.add_exchangeable(homolog_2)
self.assertEqual(str(ctx.exception),
"Cannot add 'Exchangeable' to an Exchangeable")
def test_model(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
self.assertEqual(homolog_1.model, gene_ref.model)
def test_loner(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_ref_loner = ModelGene(c_gene_ref, model, loner=True)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
homolog_2 = Exchangeable(c_gene, gene_ref_loner)
self.assertFalse(homolog_1.loner)
self.assertTrue(homolog_2.loner)
def test_multi_system(self):
model = Model("T2SS", 10)
gene_name = 'sctJ_FLG'
c_gene_ref = CoreGene(self.model_location, gene_name, self.profile_factory)
gene_ref = ModelGene(c_gene_ref, model)
gene_ref_multi_system = ModelGene(c_gene_ref, model, multi_system=True)
gene_name = 'sctJ'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
homolog_1 = Exchangeable(c_gene, gene_ref)
homolog_2 = Exchangeable(c_gene, gene_ref_multi_system)
self.assertFalse(homolog_1.multi_system)
self.assertTrue(homolog_2.multi_system)
|
