def test_get_gene(self):
system = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene = Gene(self.cfg, gene_name, system, self.profile_registry)
for meth in (system.add_forbidden_gene, system.add_accessory_gene, system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(gene, system.get_gene(gene_name))
self.assertRaises(KeyError, system.get_gene, 'bar')
homolog_name = 'sctJ'
gene_homolog = Gene(self.cfg, homolog_name, system, self.profile_registry)
homolog = Homolog(gene_homolog, gene)
gene.add_homolog(homolog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene, system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(homolog, system.get_gene(homolog_name))
analog_name = 'sctC'
gene_analog = Gene(self.cfg, analog_name, system, self.profile_registry)
analog = Analog(gene_analog, gene)
gene.add_analog(analog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene, system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene)
self.assertEqual(analog, system.get_gene(analog_name))
def test_add_homolog(self):
system_foo = System(self.cfg, "foo", 10)
system_bar = System(self.cfg, "bar", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene_ref = Gene(self.cfg, 'sctJ', system_bar, self.profile_registry)
homolog = Homolog(self.cfg, gene, gene_ref)
gene.add_homolog( homolog )
self.assertEqual(len( gene.homologs), 1)
self.assertEqual(gene.homologs[0], homolog)
def test_str(self):
"""
"""
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
system_bar = System(self.cfg, "bar", 20)
gene_homolog = Gene(self.cfg, 'sctJ', system_bar, self.profile_registry)
homolog = Homolog( gene_homolog, gene, self.cfg)
gene.add_homolog( homolog )
s = """name : sctJ_FLG
inter_gene_max_space: 10
homologs: sctJ"""
self.assertEqual( str(gene) , s )
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene_name = "gspD"
gene = Gene(self.cfg, "gspD", system, self.profile_registry)
hit_prop = {
'id': "PSAE001c01_006940",
'hit_seq_len': 803,
'replicon_name': "PSAE001c01",
'position': 694,
'i_eval': float(1.2e-234),
'score': float(779.2),
'gene_name': gene.name,
'system_name': system.name,
'profil_coverage': float(1.0),
'sequence_coverage': float(638.000000),
'begin': 104,
'end': 741
}
hit = Hit(gene, system, hit_prop['id'], hit_prop['hit_seq_len'],
hit_prop['replicon_name'], hit_prop['position'],
hit_prop['i_eval'], hit_prop['score'],
hit_prop['profil_coverage'], hit_prop['sequence_coverage'],
hit_prop['begin'], hit_prop['end'])
s = "%(id)s\t%(replicon_name)s\t%(position)d\t%(hit_seq_len)d\t%(gene_name)s\t%(system_name)s\t%(i_eval)s\t%(score)s\t%(profil_coverage)f\t%(sequence_coverage)f\t%(begin)d\t%(end)d\n" % hit_prop
self.assertEqual(s, str(hit))
def test_str(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
s = "{0} : {1}".format(gene.name, path)
self.assertEqual(str(profile), s)
def test_execute_unknown_binary(self):
self.cfg.options['hmmer_exe'] = "Nimportnaoik"
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, path)
self.assertRaises(RuntimeError, profile.execute)
def test_get_gene_ref(self):
system = System(self.cfg, "foo", 10)
gene_name = 'sctJ_FLG'
gene_ref = Gene(self.cfg, gene_name, system, self.profile_registry)
homolog_name = 'sctJ'
gene_homolg = Gene(self.cfg, homolog_name, system, self.profile_registry)
homolog = Homolog(gene_homolg, gene_ref)
gene_ref.add_homolog(homolog)
for meth in (system.add_forbidden_gene, system.add_accessory_gene, system.add_mandatory_gene):
system._mandatory_genes = []
system._accessory_genes = []
system._forbidden_genes = []
meth(gene_ref)
self.assertEqual(gene_ref, system.get_gene_ref(homolog))
self.assertIsNone(system.get_gene_ref(gene_ref))
gene_ukn = Gene(self.cfg, 'abc', system, self.profile_registry)
self.assertRaises(KeyError, system.get_gene_ref, gene_ukn)
def test_get_homologs(self):
system_foo = System(self.cfg, "foo", 10)
system_bar = System(self.cfg, "bar", 10)
gene = Gene(self.cfg, 'sctN', system_foo, self.profile_registry)
sctJ_FLG = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
sctJ = Gene(self.cfg, 'sctJ', system_bar, self.profile_registry)
homolog_1 = Homolog(sctJ_FLG, gene)
gene.add_homolog(homolog_1)
homolog_2 = Homolog(sctJ, gene)
gene.add_homolog(homolog_2)
self.assertEqual(gene.get_homologs(), [homolog_1, homolog_2] )
def test_execute(self):
system = System(self.cfg, "T2SS", 10)
gene = Gene(self.cfg, "abc", system, self.profile_registry)
path = self.profile_registry.get("abc")
profile = Profile(gene, self.cfg, 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:"
path = os.path.join(self.cfg.profile_dir, gene.name + self.cfg.profile_suffix)
self.assertTrue(l.find(path) != -1)
def test_unknow_profile(self):
system_foo = System(self.cfg, "foo", 10)
gene = Gene(self.cfg, 'sctJ_FLG', system_foo, self.profile_registry)
gene.name = "foo"
self.assertRaises(MacsypyError, profile_factory.get_profile, gene, self.cfg, self.profile_registry)