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
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 = 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 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):
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.assertFalse(profile.ga_threshold)
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("T5aSS_PF03797")
profile = Profile(gene, self.cfg, path)
self.assertTrue(profile.ga_threshold)
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(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)
# 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)
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())
# case cut-ga but no GA threshold in hmmprofile
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
