def test_get_all_definitions(self):
complex_dir = _create_fake_models_tree(self.root_models_dir,
self.complex_models)
model_loc = ModelLocation(path=complex_dir)
defs_expected = []
for def_name in self.complex_models['definitions']:
for subdef_name in self.complex_models['definitions'][def_name]:
if subdef_name.endswith('.xml'):
new_def = DefinitionLocation(
name=os.path.splitext(subdef_name)[0],
fqn=os.path.splitext(def_name)[0],
path=os.path.join(complex_dir, 'definitions', def_name,
subdef_name))
new_def.fqn = '{model_name}{sep}{def_name}{sep}{subdef_name}'.format(
model_name=model_loc.name,
sep=registries._SEPARATOR,
subdef_name=os.path.splitext(subdef_name)[0],
def_name=def_name)
defs_expected.append(new_def)
else:
for sub_subdef_name in self.complex_models['definitions'][
def_name][subdef_name]:
new_def = DefinitionLocation(
name=os.path.splitext(sub_subdef_name)[0],
fqn=os.path.splitext(def_name)[0],
path=os.path.join(complex_dir, 'definitions',
subdef_name, sub_subdef_name))
new_def.fqn = '{model_name}{sep}{def_name}{sep}{subdef_name}{sep}{sub_subdef_name}'.format(
model_name=model_loc.name,
sep=registries._SEPARATOR,
subdef_name=subdef_name,
sub_subdef_name=os.path.splitext(
sub_subdef_name)[0],
def_name=def_name)
defs_expected.append(new_def)
defs_received = model_loc.get_all_definitions()
self.assertEqual(sorted(defs_expected), sorted(defs_received))
defs_expected = []
def_root_name = 'subdef_1'
for def_name in self.complex_models['definitions'][def_root_name]:
new_def = DefinitionLocation(name=os.path.splitext(def_name)[0],
fqn=os.path.splitext(def_name)[0],
path=os.path.join(
complex_dir, 'definitions',
def_root_name, def_name))
new_def.fqn = '{model_name}{sep}{def_root_name}{sep}{def_name}'.format(
model_name=model_loc.name,
sep=registries._SEPARATOR,
def_root_name=def_root_name,
def_name=os.path.splitext(def_name)[0])
defs_expected.append(new_def)
defs_received = model_loc.get_all_definitions(
root_def_name="{model_name}{sep}{def_root_name}".format(
model_name=model_loc.name,
sep=registries._SEPARATOR,
def_root_name=def_root_name))
self.assertEqual(sorted(defs_expected), sorted(defs_received))
def test_models(self):
mr = ModelRegistry()
model_complex_expected = ModelLocation(path=self.complex_dir)
model_simple_expected = ModelLocation(path=self.simple_dir)
mr.add(model_complex_expected)
mr.add(model_simple_expected)
models_received = sorted(mr.models())
models_expected = sorted(
[model_complex_expected, model_simple_expected])
self.assertListEqual(models_received, models_expected)
def test_get_profiles_names(self):
simple_dir = _create_fake_models_tree(self.root_models_dir,
self.simple_models)
model_loc = ModelLocation(path=simple_dir)
self.assertEqual(
model_loc.get_profile(
os.path.splitext(self.simple_models['profiles'][0])[0]),
os.path.join(simple_dir, 'profiles',
self.simple_models['profiles'][0]))
def test_scan_models_dir(self):
models_location = scan_models_dir(self.cfg.models_dir())
models_location_expected = [
ModelLocation(path=self.simple_dir,
profile_suffix='.hmm',
relative_path=False),
ModelLocation(path=self.complex_dir,
profile_suffix='.hmm',
relative_path=False),
]
self.assertListEqual(sorted(models_location_expected),
sorted(models_location))
def setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(path=os.path.join(args.models_dir, model_name))
model = Model("foo/T2SS", 10)
profile_factory = ProfileFactory(cfg)
gene_name = "gspD"
self.c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
self.gene_gspd = ModelGene(self.c_gene_gspd, model)
gene_name = "sctJ"
self.c_gene_sctj = CoreGene(models_location, gene_name, profile_factory)
self.gene_sctj = ModelGene(self.c_gene_sctj, model)
model.add_mandatory_gene(self.gene_gspd)
model.add_accessory_gene(self.gene_sctj)
self.hit_1 = Hit(self.c_gene_gspd, "hit_1", 803, "replicon_id", 2, 1.0, 1.0, 1.0, 1.0, 10, 20)
self.hit_2 = Hit(self.c_gene_sctj, "hit_2", 803, "replicon_id", 3, 1.0, 1.0, 1.0, 1.0, 10, 20)
def setUp(self):
args = argparse.Namespace()
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.res_search_dir = tempfile.gettempdir()
args.log_level = 30
args.out_dir = os.path.join(args.res_search_dir,
'test_macsyfinder_Report')
if os.path.exists(args.out_dir):
shutil.rmtree(args.out_dir)
os.mkdir(args.out_dir)
seq_db = self.find_data("base", "test_base.fa")
shutil.copy(seq_db, args.out_dir)
args.sequence_db = os.path.join(args.out_dir, os.path.basename(seq_db))
self.cfg = Config(MacsyDefaults(), args)
os.mkdir(os.path.join(self.cfg.out_dir(), self.cfg.hmmer_dir()))
self.model_name = 'foo'
self.model_location = ModelLocation(
path=os.path.join(args.models_dir, self.model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
self.profile_factory = ProfileFactory(self.cfg)
idx = Indexes(self.cfg)
idx.build()
def setUp(self):
self.tmp_dir = os.path.join(tempfile.gettempdir(),
'test_macsyfinder_search_genes')
if os.path.exists(self.tmp_dir):
shutil.rmtree(self.tmp_dir)
os.mkdir(self.tmp_dir)
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_base.fa")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
args.log_level = 30
args.out_dir = os.path.join(self.tmp_dir, 'job_1')
args.res_search_dir = args.out_dir
os.mkdir(args.out_dir)
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.model_location = ModelLocation(
path=os.path.join(args.models_dir, self.model_name))
idx = Indexes(self.cfg)
idx._build_my_indexes()
self.profile_factory = ProfileFactory(self.cfg)
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 = 0
self.cfg = Config(MacsyDefaults(), args)
if os.path.exists(self.cfg.working_dir()):
shutil(self.cfg.working_dir())
os.makedirs(self.cfg.working_dir())
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 setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(path=os.path.join(args.models_dir, model_name))
model = Model("foo/T2SS", 10)
profile_factory = ProfileFactory(cfg)
gene_name = "gspD"
self.cg_gspd = CoreGene(models_location, gene_name, profile_factory)
self.mg_gspd = ModelGene(self.cg_gspd, model, loner=True, multi_system=True)
gene_name = "sctJ"
self.cg_sctj = CoreGene(models_location, gene_name, profile_factory)
self.mg_sctj = ModelGene(self.cg_sctj, model)
model.add_mandatory_gene(self.mg_gspd)
model.add_accessory_gene(self.mg_sctj)
self.chit_1 = CoreHit(self.cg_gspd, "hit_1", 803, "replicon_id", 2, 1.0, 1.0, 1.0, 1.0, 10, 20)
self.chit_2 = CoreHit(self.cg_sctj, "hit_2", 803, "replicon_id", 3, 1.0, 1.0, 1.0, 1.0, 10, 20)
self.chit_3 = CoreHit(self.cg_gspd, "hit_3", 803, "replicon_id", 10, 1.0, 1.0, 1.0, 1.0, 10, 20)
self.chit_4 = CoreHit(self.cg_gspd, "hit_4", 803, "replicon_id", 20, 1.0, 1.0, 1.0, 1.0, 10, 20)
self.mhit_1 = ModelHit(self.chit_1, self.mg_gspd, GeneStatus.MANDATORY)
self.mhit_2 = ModelHit(self.chit_2, self.mg_sctj, GeneStatus.ACCESSORY)
self.mhit_3 = ModelHit(self.chit_3, self.mg_gspd, GeneStatus.MANDATORY)
self.mhit_4 = ModelHit(self.chit_4, self.mg_gspd, GeneStatus.MANDATORY)
def test_str(self):
mr = ModelRegistry()
model_complex_expected = ModelLocation(path=self.complex_dir)
model_simple_expected = ModelLocation(path=self.simple_dir)
mr.add(model_complex_expected)
mr.add(model_simple_expected)
expected_output = """complex
/subdef_1
/def_1_1
/def_1_2
/subdef_2
/def_2_1
/def_2_2
simple
/def_1
/def_2
"""
self.assertEqual(expected_output, str(mr))
def setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
self.models_location = ModelLocation(path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model = Model(model_name, 10)
self.profile_factory = ProfileFactory(cfg)
gene_name = "gspD"
c_gene_gspd = CoreGene(self.models_location, gene_name, self.profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model, multi_system=True)
gene_name = "sctJ"
c_gene_sctj = CoreGene(self.models_location, gene_name, self.profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model, multi_system=True)
gene_name = "sctN"
c_gene_sctn = CoreGene(self.models_location, gene_name, self.profile_factory)
gene_sctn = Exchangeable(c_gene_sctn, gene_sctj)
gene_sctj.add_exchangeable(gene_sctn)
model.add_mandatory_gene(gene_gspd)
model.add_accessory_gene(gene_sctj)
# CoreHit(gene, hit_id, hit_seq_length, replicon_name, position, i_eval, score,
# profile_coverage, sequence_coverage, begin_match, end_match
# pos score
chit_1 = CoreHit(c_gene_gspd, "hit_1", 803, "replicon_id", 2, 1.0, 1.0, 1.0, 1.0, 10, 20)
chit_2 = CoreHit(c_gene_sctj, "hit_2", 803, "replicon_id", 3, 1.0, 1.0, 1.0, 1.0, 10, 20)
chit_3 = CoreHit(c_gene_gspd, "hit_3", 803, "replicon_id", 10, 1.0, 3.0, 1.0, 1.0, 10, 20)
chit_4 = CoreHit(c_gene_sctn, "hit_4", 803, "replicon_id", 14, 1.0, 4.0, 1.0, 1.0, 10, 20)
chit_5 = CoreHit(c_gene_gspd, "hit_5", 803, "replicon_id", 20, 1.0, 2.0, 1.0, 1.0, 10, 20)
self.mhit_1 = ModelHit(chit_1, gene_gspd, GeneStatus.MANDATORY)
self.mhit_2 = ModelHit(chit_2, gene_sctj, GeneStatus.ACCESSORY)
self.mhit_3 = ModelHit(chit_3, gene_gspd, GeneStatus.MANDATORY)
self.mhit_4 = ModelHit(chit_4, gene_sctn, GeneStatus.ACCESSORY)
self.mhit_5 = ModelHit(chit_5, gene_gspd, GeneStatus.MANDATORY)
self.ms_1 = MultiSystem(chit_1, gene_ref=gene_gspd, gene_status=GeneStatus.MANDATORY)
self.ms_2 = MultiSystem(chit_2, gene_ref=gene_sctj, gene_status=GeneStatus.ACCESSORY)
self.ms_3 = MultiSystem(chit_3, gene_ref=gene_gspd, gene_status=GeneStatus.MANDATORY)
self.ms_4 = MultiSystem(chit_4, gene_ref=gene_sctn, gene_status=GeneStatus.ACCESSORY)
self.ms_5 = MultiSystem(chit_5, gene_ref=gene_gspd, gene_status=GeneStatus.MANDATORY)
def test_add_get(self):
mr = ModelRegistry()
model_complex_expected = ModelLocation(path=self.complex_dir)
with self.assertRaises(KeyError) as ctx:
mr[model_complex_expected.name]
self.assertEqual(str(ctx.exception),
'"No such model definition: \'complex\'"')
mr.add(model_complex_expected)
self.assertEqual(model_complex_expected,
mr[model_complex_expected.name])
def setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
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 setUp(self) -> None:
self.args = argparse.Namespace()
self.args.sequence_db = self.find_data("base", "test_1.fasta")
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.args.res_search_dir = "blabla"
self.cfg = Config(MacsyDefaults(), self.args)
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(self.args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
self.hit_weights = HitWeight(**self.cfg.hit_weights())
def test_version_no_metadata(self):
# test new way to specify profiles and definitions
simple_dir = _create_fake_models_tree(self.root_models_dir,
self.simple_models,
metadata=False)
with self.catch_log(log_name='macsypy') as log:
model_loc = ModelLocation(path=simple_dir)
log_msg = log.get_value().strip()
self.assertEqual(model_loc.version, None)
self.assertEqual(
log_msg,
"The models package 'simple' is not versioned contact the package manager to fix it."
)
def setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
self.cfg = Config(MacsyDefaults(), args)
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(args.models_dir, self.model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
self.profile_factory = ProfileFactory(self.cfg)
def setUp(self) -> None:
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
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)
self.hit_weights = HitWeight(**self.cfg.hit_weights())
# reset the uniq id number for AbstractSetOfHits
# to have predictable results
AbstractSetOfHits._id = itertools.count(1)
def setUp(self):
self.args = argparse.Namespace()
self.args.sequence_db = self.find_data("base", "test_1.fasta")
self.args.db_type = 'gembase'
self.args.models_dir = self.find_data('models')
self.args.res_search_dir = tempfile.gettempdir()
self.args.log_level = 30
self.args.out_dir = os.path.join(self.args.res_search_dir,
'test_macsyfinder_Model')
if os.path.exists(self.args.out_dir):
shutil.rmtree(self.args.out_dir)
os.mkdir(self.args.out_dir)
self.cfg = Config(MacsyDefaults(), self.args)
self.model_name = 'foo'
self.model_location = ModelLocation(path=os.path.join(self.args.models_dir, self.model_name))
self.profile_factory = ProfileFactory(self.cfg)
def test_get_definitions(self):
simple_dir = _create_fake_models_tree(self.root_models_dir,
self.simple_models)
model_loc = ModelLocation(path=simple_dir)
model_loc._definitions = None
defs = model_loc.get_definitions()
self.assertEqual({}, defs)
model_loc._definitions = {'foo': 'bar'}
defs = model_loc.get_definitions()
self.assertListEqual(['bar'], defs)
def test_get_definition(self):
# test new way to specify profiles and definitions
simple_dir = _create_fake_models_tree(self.root_models_dir,
self.simple_models)
model_loc = ModelLocation(path=simple_dir)
def_fqn = '{}{}{}'.format(
model_loc.name, registries._SEPARATOR,
os.path.splitext(
list(self.simple_models['definitions'].keys())[0])[0])
defloc_expected_name = os.path.splitext(
list(self.simple_models['definitions'].keys())[0])[0]
defloc_expected = DefinitionLocation(
name=defloc_expected_name,
path=os.path.join(simple_dir, 'definitions',
defloc_expected_name + '.xml'))
defloc_expected.fqn = "{}{}{}".format(
model_loc.name, registries._SEPARATOR,
os.path.splitext(
list(self.simple_models['definitions'].keys())[0])[0])
defloc_received = model_loc.get_definition(def_fqn)
self.assertEqual(defloc_expected, defloc_received)
complex_dir = _create_fake_models_tree(self.root_models_dir,
self.complex_models)
model_loc = ModelLocation(path=complex_dir)
subdef_name = 'subdef_1'
def_name = 'def_1_1'
def_fqn = '{model_name}{sep}{subdef_name}{sep}{def_name}'.format(
model_name=model_loc.name,
sep=registries._SEPARATOR,
subdef_name=subdef_name,
def_name=def_name)
defloc_expected = DefinitionLocation(
name=def_name,
path=os.path.join(complex_dir, 'definitions', subdef_name,
def_name + '.xml'))
defloc_expected.fqn = def_fqn
defloc_received = model_loc.get_definition(def_fqn)
self.assertEqual(defloc_expected, defloc_received)
class TestProfile(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 = 50
self.cfg = Config(MacsyDefaults(), args)
if os.path.exists(self.cfg.working_dir()):
shutil.rmtree(self.cfg.working_dir())
os.makedirs(self.cfg.working_dir())
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:
pass
def test_len(self):
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, path)
self.assertEqual(len(profile), 501)
def test_ga_threshold(self):
# No GA threshold
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertFalse(profile.ga_threshold)
# GA threshold line ends with ;
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertTrue(profile.ga_threshold)
# GA threshold line do NOT ends with ;
gene_name = 'PF05930.13'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
profile = Profile(gene, self.cfg, path)
self.assertTrue(profile.ga_threshold)
# GA threshold invalid format string instead float
gene_name = 'bad_GA'
with self.catch_log(log_name='macsypy'):
# When a CoreGene is created a Profile is automatically instanciated
# So I mute the log to do not polute output
c_gene = CoreGene(self.model_location, gene_name,
self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
with self.catch_log(log_name='macsypy') as log:
profile = Profile(gene, self.cfg, path)
catch_msg = log.get_value().strip()
self.assertFalse(profile.ga_threshold)
self.assertEqual(
catch_msg,
"bad_GA GA score is not well formatted expected 2 floats got ''22.00'' ''23.00''.\n"
"GA score will not used for gene 'bad_GA'.")
# GA threshold invalid format only one score
gene_name = 'bad_GA_2'
with self.catch_log(log_name='macsypy'):
# When a CoreGene is created a Profile is automatically instanciated
# So I mute the log to do not polute output
c_gene = CoreGene(self.model_location, gene_name,
self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile(gene_name)
with self.catch_log(log_name='macsypy') as log:
profile = Profile(gene, self.cfg, path)
catch_msg = log.get_value().strip()
self.assertFalse(profile.ga_threshold)
self.assertEqual(
catch_msg,
"bad_GA_2 GA score is not well formatted. expected: 'GA float float' got 'GA 22.00'.\n"
"GA score will not used for gene 'bad_GA_2'.")
def test_str(self):
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, path)
s = "{0} : {1}".format(gene.name, path)
self.assertEqual(str(profile), s)
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_with_GA(self):
for db_type in ("gembase", "ordered_replicon", "unordered"):
self.cfg._set_db_type(db_type)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name,
self.profile_factory)
gene = ModelGene(c_gene, model)
# case GA threshold in profile
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, self.cfg, profile_path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(
first_l.startswith(
"# hmmsearch :: search profile(s) against a sequence database"
))
for i in range(5):
# skip 4 lines
l = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(l.find(profile_path) != -1)
for i in range(3):
# skip 2 lines
l = hmmer_raw_out_file.readline()
self.assertEqual(
"# model-specific thresholding: GA cutoffs", l.strip())
# test if profile is executed only once per run
report_bis = profile.execute()
self.assertIs(report, report_bis)
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_protected_path(self):
# create a hmmdir with space in name
self.cfg.hmmer_dir = lambda: 'hmmer results'
# create sequence_db path with space in path
seq_path = os.path.join(self.cfg.working_dir(), "test test1.fasta")
shutil.copyfile(self.find_data("base", "test_1.fasta"), seq_path)
self.cfg._set_sequence_db(seq_path)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
# case GA threshold in profile
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, self.cfg, profile_path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(
first_l.startswith(
"# hmmsearch :: search profile(s) against a sequence database"
))
for i in range(5):
# skip 4 lines
l = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(l.find(profile_path) != -1)
for i in range(3):
# skip 2 lines
l = hmmer_raw_out_file.readline()
self.assertEqual("# model-specific thresholding: GA cutoffs",
l.strip())
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_w_GA_n_nocutga(self):
# case GA threshold in profile but --no-cut-ga is set
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 = 0
args.e_value_search = 0.5
args.no_cut_ga = True
cfg = Config(MacsyDefaults(), args)
model = Model("foo/T2SS", 10)
gene_name = 'T5aSS_PF03797'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
profile_path = self.model_location.get_profile("T5aSS_PF03797")
profile = Profile(gene, cfg, profile_path)
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
for i in range(9):
l = hmmer_raw_out_file.readline()
self.assertEqual(
"# sequence reporting threshold: E-value <= 0.5", l.strip())
@unittest.skipIf(not which('hmmsearch'), 'hmmsearch not found in PATH')
def test_execute_hmm_wo_GA(self):
# case cut-ga but no GA threshold in hmmprofile
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
# case -cut-ga and GA threshold in profile
profile_path = self.model_location.get_profile("abc")
profile = Profile(gene, self.cfg, profile_path)
with self.catch_log() as log:
report = profile.execute()
hmmer_raw_out = profile.hmm_raw_output
with open(hmmer_raw_out, 'r') as hmmer_raw_out_file:
first_l = hmmer_raw_out_file.readline()
# a hmmsearch output file has been produced
self.assertTrue(
first_l.startswith(
"# hmmsearch :: search profile(s) against a sequence database"
))
for i in range(5):
# skip 4 lines
l = hmmer_raw_out_file.readline()
# a hmmsearch used the abc profile line should become with: "# query HMM file: {the path tp hmm profile used}"
self.assertTrue(l.find(profile_path) != -1)
for i in range(3):
# skip 2 lines
l = hmmer_raw_out_file.readline()
self.assertEqual(
'# sequence reporting threshold: E-value <= 0.1', l.strip())
def test_execute_unknown_binary(self):
self.cfg._options['hmmer'] = "Nimportnaoik"
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc", )
profile = Profile(gene, self.cfg, path)
with self.catch_log():
with self.assertRaises(RuntimeError):
profile.execute()
def test_execute_hmmer_failed(self):
fake_hmmer = os.path.join(tempfile.gettempdir(), 'hmmer_failed')
with open(fake_hmmer, 'w') as hmmer:
hmmer.write("""#! {}
import sys
sys.exit(127)
""".format(sysconfig.sys.executable))
try:
os.chmod(hmmer.name, 0o755)
self.cfg._options['hmmer'] = hmmer.name
model = Model("foo/T2SS", 10)
gene_name = 'abc'
c_gene = CoreGene(self.model_location, gene_name,
self.profile_factory)
gene = ModelGene(c_gene, model)
path = self.model_location.get_profile("abc", )
profile = Profile(gene, self.cfg, path)
with self.catch_log():
with self.assertRaisesRegex(
RuntimeError, "an error occurred during Hmmer "
"execution: command = .* : return code = 127 .*"
) as ctx:
profile.execute()
finally:
try:
os.unlink(fake_hmmer)
except Exception:
pass
def test_SystemSerializer_str(self):
model_name = 'foo'
model_location = ModelLocation(
path=os.path.join(self.cfg.models_dir(), model_name))
model_A = Model("foo/A", 10)
model_B = Model("foo/B", 10)
c_gene_sctn_flg = CoreGene(model_location, "sctN_FLG",
self.profile_factory)
gene_sctn_flg = ModelGene(c_gene_sctn_flg, model_B)
c_gene_sctj_flg = CoreGene(model_location, "sctJ_FLG",
self.profile_factory)
gene_sctj_flg = ModelGene(c_gene_sctj_flg, model_B)
c_gene_flgB = CoreGene(model_location, "flgB", self.profile_factory)
c_gene_tadZ = CoreGene(model_location, "tadZ", self.profile_factory)
gene_tadZ = ModelGene(c_gene_tadZ, model_B)
c_gene_sctn = CoreGene(model_location, "sctN", self.profile_factory)
gene_sctn = ModelGene(c_gene_sctn, model_A)
gene_sctn_hom = Exchangeable(c_gene_sctn_flg, gene_sctn)
gene_sctn.add_exchangeable(gene_sctn_hom)
c_gene_sctj = CoreGene(model_location, "sctJ", self.profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model_A)
gene_sctj_an = Exchangeable(c_gene_sctj_flg, gene_sctj)
gene_sctj.add_exchangeable(gene_sctj_an)
c_gene_gspd = CoreGene(model_location, "gspD", self.profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model_A)
gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd)
gene_gspd.add_exchangeable(gene_gspd_an)
c_gene_abc = CoreGene(model_location, "abc", self.profile_factory)
gene_abc = ModelGene(c_gene_abc, model_A)
gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc)
gene_abc.add_exchangeable(gene_abc_ho)
model_A.add_mandatory_gene(gene_sctn)
model_A.add_mandatory_gene(gene_sctj)
model_A.add_accessory_gene(gene_gspd)
model_A.add_forbidden_gene(gene_abc)
model_B.add_mandatory_gene(gene_sctn_flg)
model_B.add_mandatory_gene(gene_sctj_flg)
model_B.add_accessory_gene(gene_gspd)
model_B.add_accessory_gene(gene_tadZ)
h_sctj = Hit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctn = Hit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_gspd = Hit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctj_flg = Hit(c_gene_sctj_flg, "hit_sctj_flg", 803, "replicon_id",
1, 1.0, 1.0, 1.0, 1.0, 10, 20)
h_tadZ = Hit(c_gene_tadZ, "hit_tadZ", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
model_A._min_mandatory_genes_required = 2
model_A._min_genes_required = 2
c1 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY),
ValidHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY)
], model_A, self.hit_weights)
c2 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY)
], model_A, self.hit_weights)
model_B._min_mandatory_genes_required = 1
model_B._min_genes_required = 2
c3 = Cluster([
ValidHit(h_sctj_flg, gene_sctj_flg, GeneStatus.MANDATORY),
ValidHit(h_tadZ, gene_tadZ, GeneStatus.ACCESSORY),
ValidHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY)
], model_B, self.hit_weights)
sys_A = System(model_A, [c1, c2], self.cfg.redundancy_penalty())
sys_A.id = "sys_id_A"
sys_B = System(model_B, [c3], self.cfg.redundancy_penalty())
sys_B.id = "sys_id_B"
hit_multi_sys_tracker = HitSystemTracker([sys_A, sys_B])
system_serializer = TxtSystemSerializer()
sys_str = f"""system id = {sys_A.id}
model = foo/A
replicon = replicon_id
clusters = [('hit_sctj', 'sctJ', 1), ('hit_sctn', 'sctN', 1), ('hit_gspd', 'gspD', 1)], [('hit_sctj', 'sctJ', 1), ('hit_sctn', 'sctN', 1)]
occ = 2
wholeness = 1.000
loci nb = 2
score = 1.500
mandatory genes:
\t- sctN: 2 (sctN, sctN)
\t- sctJ: 2 (sctJ, sctJ)
accessory genes:
\t- gspD: 1 (gspD [sys_id_B])
neutral genes:
"""
self.assertEqual(
sys_str, system_serializer.serialize(sys_A, hit_multi_sys_tracker))
def test_str(self):
simple_dir = _create_fake_models_tree(self.root_models_dir,
self.simple_models)
model_loc = ModelLocation(path=simple_dir)
model_loc.name = 'foo20'
self.assertEqual('foo20', str(model_loc))
def test_systems_to_txt(self):
system_str = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# No Systems found
"""
f_out = StringIO()
track_multi_systems_hit = HitSystemTracker([])
systems_to_txt([], track_multi_systems_hit, f_out)
self.assertMultiLineEqual(system_str, f_out.getvalue())
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'gembase'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model = Model("foo/T2SS", 10)
# test if id is well incremented
gene_name = "gspD"
c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model)
model.add_mandatory_gene(gene_gspd)
gene_name = "sctJ"
c_gene_sctj = CoreGene(models_location, gene_name, profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model)
model.add_accessory_gene(gene_sctj)
hit_1 = Hit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_1 = ValidHit(hit_1, gene_gspd, GeneStatus.MANDATORY)
hit_2 = Hit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_2 = ValidHit(hit_2, gene_sctj, GeneStatus.ACCESSORY)
system_1 = System(model, [
Cluster([v_hit_1, v_hit_2], model, HitWeight(**cfg.hit_weights()))
], cfg.redundancy_penalty())
system_str = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Systems found:
system id = replicon_id_T2SS_{next(System._id) - 1}
model = foo/T2SS
replicon = replicon_id
clusters = [('hit_1', 'gspD', 1), ('hit_2', 'sctJ', 1)]
occ = 1
wholeness = 1.000
loci nb = 1
score = 1.500
mandatory genes:
\t- gspD: 1 (gspD)
accessory genes:
\t- sctJ: 1 (sctJ)
neutral genes:
============================================================
"""
f_out = StringIO()
track_multi_systems_hit = HitSystemTracker([system_1])
systems_to_txt([system_1], track_multi_systems_hit, f_out)
self.assertMultiLineEqual(system_str, f_out.getvalue())
def test_unnlikely_systems_to_txt(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'unordered'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model = Model("foo/T2SS", 10)
# test if id is well incremented
gene_name = "gspD"
c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model)
model.add_mandatory_gene(gene_gspd)
gene_name = "sctJ"
c_gene_sctj = CoreGene(models_location, gene_name, profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model)
model.add_accessory_gene(gene_sctj)
gene_name = "sctC"
c_gene_sctc = CoreGene(models_location, gene_name, profile_factory)
gene_sctc = ModelGene(c_gene_sctc, model)
model.add_neutral_gene(gene_sctc)
gene_name = "tadZ"
c_gene_tadz = CoreGene(models_location, gene_name, profile_factory)
gene_tadz = ModelGene(c_gene_tadz, model)
model.add_forbidden_gene(gene_tadz)
hit_1 = Hit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_1 = ValidHit(hit_1, gene_gspd, GeneStatus.MANDATORY)
hit_2 = Hit(c_gene_sctj, "hit_2", 804, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_2 = ValidHit(hit_2, gene_sctj, GeneStatus.ACCESSORY)
hit_3 = Hit(c_gene_sctc, "hit_3", 805, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_3 = ValidHit(hit_3, gene_sctc, GeneStatus.NEUTRAL)
hit_4 = Hit(c_gene_tadz, "hit_4", 806, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_4 = ValidHit(hit_4, gene_tadz, GeneStatus.FORBIDDEN)
reason = "why it not a system"
system_1 = UnlikelySystem(model, [v_hit_1], [v_hit_2], [v_hit_3],
[v_hit_4], reason)
exp_txt = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Unlikely Systems found:
This replicon probably not contains a system foo/T2SS:
{reason}
system id = replicon_id_T2SS_1
model = foo/T2SS
replicon = replicon_id
hits = [('hit_1', 'gspD', 1), ('hit_2', 'sctJ', 1), ('hit_3', 'sctC', 1), ('hit_4', 'tadZ', 1)]
wholeness = 1.000
mandatory genes:
\t- gspD: 1 (gspD)
accessory genes:
\t- sctJ: 1 (sctJ)
neutral genes:
\t- sctC: 1 (sctC)
forbidden genes:
\t- tadZ: 1 (tadZ)
Use ordered replicon to have better prediction.
============================================================
"""
f_out = StringIO()
unlikely_systems_to_txt([system_1], f_out)
self.assertMultiLineEqual(exp_txt, f_out.getvalue())
f_out = StringIO()
unlikely_systems_to_txt([], f_out)
expected_out = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# No Unlikely Systems found
"""
self.assertEqual(expected_out, f_out.getvalue())
def test_likely_systems_to_tsv(self):
args = argparse.Namespace()
args.sequence_db = self.find_data("base", "test_1.fasta")
args.db_type = 'unordered'
args.models_dir = self.find_data('models')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model = Model("foo/T2SS", 10)
# test if id is well incremented
gene_name = "gspD"
c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model)
model.add_mandatory_gene(gene_gspd)
gene_name = "sctJ"
c_gene_sctj = CoreGene(models_location, gene_name, profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model)
model.add_accessory_gene(gene_sctj)
gene_name = "sctC"
c_gene_sctc = CoreGene(models_location, gene_name, profile_factory)
gene_sctc = ModelGene(c_gene_sctc, model)
model.add_neutral_gene(gene_sctc)
gene_name = "tadZ"
c_gene_tadz = CoreGene(models_location, gene_name, profile_factory)
gene_tadz = ModelGene(c_gene_tadz, model)
model.add_forbidden_gene(gene_tadz)
hit_1 = Hit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_1 = ValidHit(hit_1, gene_gspd, GeneStatus.MANDATORY)
hit_2 = Hit(c_gene_sctj, "hit_2", 804, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_2 = ValidHit(hit_2, gene_sctj, GeneStatus.ACCESSORY)
hit_3 = Hit(c_gene_sctc, "hit_3", 805, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_3 = ValidHit(hit_3, gene_sctc, GeneStatus.NEUTRAL)
hit_4 = Hit(c_gene_tadz, "hit_4", 806, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_4 = ValidHit(hit_4, gene_tadz, GeneStatus.FORBIDDEN)
system_1 = LikelySystem(model, [v_hit_1], [v_hit_2], [v_hit_3],
[v_hit_4])
sol_tsv = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Likely Systems found:"""
sol_tsv += "\n\n"
sol_tsv += "\t".join([
"replicon", "hit_id", "gene_name", "hit_pos", "model_fqn",
"sys_id", "sys_wholeness", "hit_gene_ref", "hit_status",
"hit_seq_len", "hit_i_eval", "hit_score", "hit_profile_cov",
"hit_seq_cov", "hit_begin_match", "hit_end_match", "used_in"
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
"replicon_id", "hit_1", "gspD", "1", "foo/T2SS",
"replicon_id_T2SS_1", "1.000", "gspD", "mandatory", "803", "1.0",
"1.000", "1.000", "1.000", "10", "20", ""
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
"replicon_id", "hit_2", "sctJ", "1", "foo/T2SS",
"replicon_id_T2SS_1", "1.000", "sctJ", "accessory", "804", "1.0",
"1.000", "1.000", "1.000", "10", "20", ""
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
"replicon_id", "hit_4", "tadZ", "1", "foo/T2SS",
"replicon_id_T2SS_1", "1.000", "tadZ", "forbidden", "806", "1.0",
"1.000", "1.000", "1.000", "10", "20", ""
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
"replicon_id", "hit_3", "sctC", "1", "foo/T2SS",
"replicon_id_T2SS_1", "1.000", "sctC", "neutral", "805", "1.0",
"1.000", "1.000", "1.000", "10", "20", ""
])
sol_tsv += "\n"
sol_tsv += "\n"
f_out = StringIO()
track_multi_systems_hit = HitSystemTracker([system_1])
likely_systems_to_tsv([system_1], track_multi_systems_hit, f_out)
self.assertMultiLineEqual(sol_tsv, f_out.getvalue())
f_out = StringIO()
likely_systems_to_tsv([], track_multi_systems_hit, f_out)
expected_out = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# No Likely Systems found
"""
self.assertEqual(expected_out, f_out.getvalue())
def test_rejected_clst_to_txt(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 = "blabla"
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
profile_factory = ProfileFactory(cfg)
model = Model("foo/T2SS", 11)
gene_name = "gspD"
c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
gene_1 = ModelGene(c_gene_gspd, model)
gene_name = "sctC"
c_gene_sctc = CoreGene(models_location, gene_name, profile_factory)
gene_2 = ModelGene(c_gene_sctc, model)
model.add_mandatory_gene(gene_1)
model.add_accessory_gene(gene_2)
# Hit(gene, model, hit_id, hit_seq_length, replicon_name, position, i_eval, score,
# profile_coverage, sequence_coverage, begin_match, end_match
h10 = Hit(c_gene_gspd, "h10", 10, "replicon_1", 10, 1.0, 10.0, 1.0,
1.0, 10, 20)
v_h10 = ValidHit(h10, gene_1, GeneStatus.MANDATORY)
h20 = Hit(c_gene_sctc, "h20", 10, "replicon_1", 20, 1.0, 20.0, 1.0,
1.0, 10, 20)
v_h20 = ValidHit(h20, gene_2, GeneStatus.ACCESSORY)
h40 = Hit(c_gene_gspd, "h10", 10, "replicon_1", 40, 1.0, 10.0, 1.0,
1.0, 10, 20)
v_h40 = ValidHit(h40, gene_1, GeneStatus.MANDATORY)
h50 = Hit(c_gene_sctc, "h20", 10, "replicon_1", 50, 1.0, 20.0, 1.0,
1.0, 10, 20)
v_h50 = ValidHit(h50, gene_2, GeneStatus.ACCESSORY)
hit_weights = HitWeight(**cfg.hit_weights())
c1 = Cluster([v_h10, v_h20], model, hit_weights)
c2 = Cluster([v_h40, v_h50], model, hit_weights)
r_c = RejectedClusters(model, [c1, c2],
["The reasons to reject this clusters"])
rej_clst_str = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Rejected clusters:
Cluster:
- model = T2SS
- replicon = replicon_1
- hits = (h10, gspD, 10), (h20, sctC, 20)
Cluster:
- model = T2SS
- replicon = replicon_1
- hits = (h10, gspD, 40), (h20, sctC, 50)
These clusters have been rejected because:
\t- The reasons to reject this clusters
============================================================
"""
f_out = StringIO()
rejected_clst_to_txt([r_c], f_out)
self.maxDiff = None
self.assertMultiLineEqual(rej_clst_str, f_out.getvalue())
rej_clst_str = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# No Rejected clusters
"""
f_out = StringIO()
rejected_clst_to_txt([], f_out)
self.assertMultiLineEqual(rej_clst_str, f_out.getvalue())
def test_solutions_to_tsv(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')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model_A = Model("foo/A", 10)
model_B = Model("foo/B", 10)
model_C = Model("foo/C", 10)
c_gene_sctn_flg = CoreGene(models_location, "sctN_FLG",
profile_factory)
gene_sctn_flg = ModelGene(c_gene_sctn_flg, model_B)
c_gene_sctj_flg = CoreGene(models_location, "sctJ_FLG",
profile_factory)
gene_sctj_flg = ModelGene(c_gene_sctj_flg, model_B)
c_gene_flgB = CoreGene(models_location, "flgB", profile_factory)
gene_flgB = ModelGene(c_gene_flgB, model_B)
c_gene_tadZ = CoreGene(models_location, "tadZ", profile_factory)
gene_tadZ = ModelGene(c_gene_tadZ, model_B)
c_gene_sctn = CoreGene(models_location, "sctN", profile_factory)
gene_sctn = ModelGene(c_gene_sctn, model_A)
gene_sctn_hom = Exchangeable(c_gene_sctn_flg, gene_sctn)
gene_sctn.add_exchangeable(gene_sctn_hom)
c_gene_sctj = CoreGene(models_location, "sctJ", profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model_A)
gene_sctj_an = Exchangeable(c_gene_sctj_flg, gene_sctj)
gene_sctj.add_exchangeable(gene_sctj_an)
c_gene_gspd = CoreGene(models_location, "gspD", profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model_A)
gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd)
gene_gspd.add_exchangeable(gene_gspd_an)
c_gene_abc = CoreGene(models_location, "abc", profile_factory)
gene_abc = ModelGene(c_gene_abc, model_A)
gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc)
gene_abc.add_exchangeable(gene_abc_ho)
model_A.add_mandatory_gene(gene_sctn)
model_A.add_mandatory_gene(gene_sctj)
model_A.add_accessory_gene(gene_gspd)
model_A.add_forbidden_gene(gene_abc)
model_B.add_mandatory_gene(gene_sctn_flg)
model_B.add_mandatory_gene(gene_sctj_flg)
model_B.add_accessory_gene(gene_flgB)
model_B.add_accessory_gene(gene_tadZ)
model_C.add_mandatory_gene(gene_sctn_flg)
model_C.add_mandatory_gene(gene_sctj_flg)
model_C.add_mandatory_gene(gene_flgB)
model_C.add_accessory_gene(gene_tadZ)
model_C.add_accessory_gene(gene_gspd)
h_sctj = Hit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctn = Hit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_gspd = Hit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctj_flg = Hit(c_gene_sctj_flg, "hit_sctj_flg", 803, "replicon_id",
1, 1.0, 1.0, 1.0, 1.0, 10, 20)
h_flgB = Hit(c_gene_flgB, "hit_flgB", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_tadZ = Hit(c_gene_tadZ, "hit_tadZ", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
model_A._min_mandatory_genes_required = 2
model_A._min_genes_required = 2
hit_weights = HitWeight(**cfg.hit_weights())
c1 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY),
ValidHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY)
], model_A, hit_weights)
c2 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY)
], model_A, hit_weights)
model_B._min_mandatory_genes_required = 1
model_B._min_genes_required = 2
c3 = Cluster([
ValidHit(h_sctj_flg, gene_sctj_flg, GeneStatus.MANDATORY),
ValidHit(h_tadZ, gene_tadZ, GeneStatus.ACCESSORY),
ValidHit(h_flgB, gene_flgB, GeneStatus.ACCESSORY)
], model_B, hit_weights)
model_C._min_mandatory_genes_required = 1
model_C._min_genes_required = 2
c4 = Cluster([
ValidHit(h_sctj_flg, gene_sctj_flg, GeneStatus.MANDATORY),
ValidHit(h_tadZ, gene_tadZ, GeneStatus.ACCESSORY),
ValidHit(h_flgB, gene_flgB, GeneStatus.MANDATORY),
ValidHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY)
], model_C, hit_weights)
sys_A = System(model_A, [c1, c2], cfg.redundancy_penalty())
sys_A.id = "sys_id_A"
sys_B = System(model_B, [c3], cfg.redundancy_penalty())
sys_B.id = "sys_id_B"
sys_C = System(model_C, [c4], cfg.redundancy_penalty())
sys_C.id = "sys_id_C"
sol_1 = [sys_A, sys_B]
sol_2 = [sys_A, sys_C]
sol_id_1 = '1'
sol_id_2 = '2'
sol_tsv = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Systems found:
"""
sol_tsv += "\t".join([
"sol_id", "replicon", "hit_id", "gene_name", "hit_pos",
"model_fqn", "sys_id", "sys_loci", "sys_wholeness", "sys_score",
"sys_occ", "hit_gene_ref", "hit_status", "hit_seq_len",
"hit_i_eval", "hit_score", "hit_profile_cov", "hit_seq_cov",
"hit_begin_match", "hit_end_match", "used_in"
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_gspd', 'gspD', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'gspD', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_sctj_flg', 'sctJ_FLG', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'sctJ_FLG', 'mandatory',
'803', '1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_tadZ', 'tadZ', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'tadZ', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_1, 'replicon_id', 'hit_flgB', 'flgB', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'flgB', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_gspd', 'gspD', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'gspD', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_sctj_flg', 'sctJ_FLG', '1', 'foo/C',
'sys_id_C', '1', '0.800', '3.000', '1', 'sctJ_FLG', 'mandatory',
'803', '1.0', '1.000', '1.000', '1.000', '10', '20', 'sys_id_B'
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_tadZ', 'tadZ', '1', 'foo/C',
'sys_id_C', '1', '0.800', '3.000', '1', 'tadZ', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', 'sys_id_B'
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_flgB', 'flgB', '1', 'foo/C',
'sys_id_C', '1', '0.800', '3.000', '1', 'flgB', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', 'sys_id_B'
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id_2, 'replicon_id', 'hit_gspd', 'gspD', '1', 'foo/C',
'sys_id_C', '1', '0.800', '3.000', '1', 'gspD', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', 'sys_id_A'
])
sol_tsv += "\n"
sol_tsv += "\n"
f_out = StringIO()
hit_multi_sys_tracker = HitSystemTracker([sys_A, sys_B])
solutions_to_tsv([sol_1, sol_2], hit_multi_sys_tracker, f_out)
self.assertMultiLineEqual(sol_tsv, f_out.getvalue())
def test_systems_to_tsv(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')
cfg = Config(MacsyDefaults(), args)
model_name = 'foo'
models_location = ModelLocation(
path=os.path.join(args.models_dir, model_name))
# we need to reset the ProfileFactory
# because it's a like a singleton
# so other tests are influenced by ProfileFactory and it's configuration
# for instance search_genes get profile without hmmer_exe
profile_factory = ProfileFactory(cfg)
model = Model("foo/T2SS", 10)
gene_name = "gspD"
c_gene_gspd = CoreGene(models_location, gene_name, profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model)
model.add_mandatory_gene(gene_gspd)
gene_name = "sctJ"
c_gene_sctj = CoreGene(models_location, gene_name, profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model)
model.add_accessory_gene(gene_sctj)
hit_1 = Hit(c_gene_gspd, "hit_1", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_1 = ValidHit(hit_1, gene_gspd, GeneStatus.MANDATORY)
hit_2 = Hit(c_gene_sctj, "hit_2", 803, "replicon_id", 1, 1.0, 1.0, 1.0,
1.0, 10, 20)
v_hit_2 = ValidHit(hit_2, gene_sctj, GeneStatus.ACCESSORY)
system_1 = System(model, [
Cluster([v_hit_1, v_hit_2], model, HitWeight(**cfg.hit_weights()))
], cfg.redundancy_penalty())
system_tsv = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# Systems found:
"""
system_tsv += "\t".join([
"replicon", "hit_id", "gene_name", "hit_pos", "model_fqn",
"sys_id", "sys_loci", "sys_wholeness", "sys_score", "sys_occ",
"hit_gene_ref", "hit_status", "hit_seq_len", "hit_i_eval",
"hit_score", "hit_profile_cov", "hit_seq_cov", "hit_begin_match",
"hit_end_match", "used_in"
])
system_tsv += "\n"
system_tsv += "\t".join([
"replicon_id", "hit_1", "gspD", "1", "foo/T2SS", system_1.id, "1",
"1.000", "1.500", "1", "gspD", "mandatory", "803", "1.0", "1.000",
"1.000", "1.000", "10", "20", ""
])
system_tsv += "\n"
system_tsv += "\t".join([
"replicon_id", "hit_2", "sctJ", "1", "foo/T2SS", system_1.id, "1",
"1.000", "1.500", "1", "sctJ", "accessory", "803", "1.0", "1.000",
"1.000", "1.000", "10", "20", ""
])
system_tsv += "\n\n"
f_out = StringIO()
track_multi_systems_hit = HitSystemTracker([system_1])
systems_to_tsv([system_1], track_multi_systems_hit, f_out)
self.assertMultiLineEqual(system_tsv, f_out.getvalue())
# test No system found
system_str = f"""# macsyfinder {macsypy.__version__}
# {' '.join(sys.argv)}
# No Systems found
"""
f_out = StringIO()
track_multi_systems_hit = HitSystemTracker([])
systems_to_tsv([], track_multi_systems_hit, f_out)
self.assertMultiLineEqual(system_str, f_out.getvalue())
def test_SolutionSerializer_tsv(self):
model_name = 'foo'
model_location = ModelLocation(
path=os.path.join(self.cfg.models_dir(), model_name))
model_A = Model("foo/A", 10)
model_B = Model("foo/B", 10)
c_gene_sctn_flg = CoreGene(model_location, "sctN_FLG",
self.profile_factory)
gene_sctn_flg = ModelGene(c_gene_sctn_flg, model_B)
c_gene_sctj_flg = CoreGene(model_location, "sctJ_FLG",
self.profile_factory)
gene_sctj_flg = ModelGene(c_gene_sctj_flg, model_B)
c_gene_flgB = CoreGene(model_location, "flgB", self.profile_factory)
gene_flgB = ModelGene(c_gene_flgB, model_B)
c_gene_tadZ = CoreGene(model_location, "tadZ", self.profile_factory)
gene_tadZ = ModelGene(c_gene_tadZ, model_B)
c_gene_sctn = CoreGene(model_location, "sctN", self.profile_factory)
gene_sctn = ModelGene(c_gene_sctn, model_A)
gene_sctn_hom = Exchangeable(c_gene_sctn_flg, gene_sctn)
gene_sctn.add_exchangeable(gene_sctn_hom)
c_gene_sctj = CoreGene(model_location, "sctJ", self.profile_factory)
gene_sctj = ModelGene(c_gene_sctj, model_A)
gene_sctj_an = Exchangeable(c_gene_sctj_flg, gene_sctj)
gene_sctj.add_exchangeable(gene_sctj_an)
c_gene_gspd = CoreGene(model_location, "gspD", self.profile_factory)
gene_gspd = ModelGene(c_gene_gspd, model_A)
gene_gspd_an = Exchangeable(c_gene_flgB, gene_gspd)
gene_gspd.add_exchangeable(gene_gspd_an)
c_gene_abc = CoreGene(model_location, "abc", self.profile_factory)
gene_abc = ModelGene(c_gene_abc, model_A)
gene_abc_ho = Exchangeable(c_gene_tadZ, gene_abc)
gene_abc.add_exchangeable(gene_abc_ho)
model_A.add_mandatory_gene(gene_sctn)
model_A.add_mandatory_gene(gene_sctj)
model_A.add_accessory_gene(gene_gspd)
model_A.add_forbidden_gene(gene_abc)
model_B.add_mandatory_gene(gene_sctn_flg)
model_B.add_mandatory_gene(gene_sctj_flg)
model_B.add_accessory_gene(gene_flgB)
model_B.add_accessory_gene(gene_tadZ)
h_sctj = Hit(c_gene_sctj, "hit_sctj", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctn = Hit(c_gene_sctn, "hit_sctn", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_gspd = Hit(c_gene_gspd, "hit_gspd", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_sctj_flg = Hit(c_gene_sctj_flg, "hit_sctj_flg", 803, "replicon_id",
1, 1.0, 1.0, 1.0, 1.0, 10, 20)
h_flgB = Hit(c_gene_flgB, "hit_flgB", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
h_tadZ = Hit(c_gene_tadZ, "hit_tadZ", 803, "replicon_id", 1, 1.0, 1.0,
1.0, 1.0, 10, 20)
model_A._min_mandatory_genes_required = 2
model_A._min_genes_required = 2
c1 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY),
ValidHit(h_gspd, gene_gspd, GeneStatus.ACCESSORY)
], model_A, self.hit_weights)
c2 = Cluster([
ValidHit(h_sctj, gene_sctj, GeneStatus.MANDATORY),
ValidHit(h_sctn, gene_sctn, GeneStatus.MANDATORY)
], model_A, self.hit_weights)
model_B._min_mandatory_genes_required = 1
model_B._min_genes_required = 2
c3 = Cluster([
ValidHit(h_sctj_flg, gene_sctj_flg, GeneStatus.MANDATORY),
ValidHit(h_tadZ, gene_tadZ, GeneStatus.ACCESSORY),
ValidHit(h_flgB, gene_flgB, GeneStatus.ACCESSORY)
], model_B, self.hit_weights)
sys_A = System(model_A, [c1, c2], self.cfg.redundancy_penalty())
sys_A.id = "sys_id_A"
sys_B = System(model_B, [c3], self.cfg.redundancy_penalty())
sys_B.id = "sys_id_B"
sol = [sys_A, sys_B]
sol_id = '12'
hit_multi_sys_tracker = HitSystemTracker([sys_A, sys_B])
system_serializer = TsvSolutionSerializer()
sol_tsv = '\t'.join([
sol_id, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_gspd', 'gspD', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'gspD', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_sctj', 'sctJ', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctJ', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_sctn', 'sctN', '1', 'foo/A',
'sys_id_A', '2', '1.000', '1.500', '2', 'sctN', 'mandatory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_sctj_flg', 'sctJ_FLG', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'sctJ_FLG', 'mandatory',
'803', '1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_tadZ', 'tadZ', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'tadZ', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += '\t'.join([
sol_id, 'replicon_id', 'hit_flgB', 'flgB', '1', 'foo/B',
'sys_id_B', '1', '0.750', '2.000', '1', 'flgB', 'accessory', '803',
'1.0', '1.000', '1.000', '1.000', '10', '20', ''
])
sol_tsv += "\n"
sol_tsv += "\n"
ser = system_serializer.serialize(sol, sol_id, hit_multi_sys_tracker)
self.assertEqual(ser, sol_tsv)
