def test_find_my_indexes(self):
idx = Indexes(self.cfg)
self.assertIsNone(idx.find_my_indexes())
new_idx = os.path.join(os.path.dirname(self.cfg.sequence_db),
idx.name + ".idx")
open(new_idx, 'w')
self.assertEqual(idx.find_my_indexes(), new_idx)
def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(my_idx, os.path.join(os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"))
self.assertEqual(hmmer_idx, [self.cfg.sequence_db + suffix for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')])
def test_build_no_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
self.assertEqual(my_idx, os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"))
self.assertEqual( hmmer_idx , [ self.cfg.sequence_db + suffix for suffix in ('.phr', '.pin', '.psd', '.psi', '.psq')])
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
#put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx +[my_idx]:
self.assertEqual(os.path.getsize(f), 0)
def test_build_force(self):
# put fake hmmer indexes
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join( self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
idx.build(force=True)
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx + [my_idx]:
self.assertNotEqual(os.path.getsize(f), 0)
def test_build_with_idx(self):
if not which('makeblastdb') and which('formatdb'):
self.cfg.options['index_db_exe'] = 'formatdb'
# put fake hmmer indexes
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
idx = Indexes(self.cfg)
new_idx = open(os.path.join( os.path.dirname(self.cfg.sequence_db), idx.name + ".idx"), 'w')
idx.build()
my_idx = idx.find_my_indexes()
hmmer_idx = idx.find_hmmer_indexes()
for f in hmmer_idx + [my_idx]:
self.assertEqual(os.path.getsize(f), 0)
def test_fill_my_db(self):
gene_name = "gspD"
c_gene = CoreGene(self.model_location, gene_name, self.profile_factory)
report_path = os.path.join(self.cfg.working_dir(),
gene_name + self.cfg.res_search_suffix())
report = GembaseHMMReport(c_gene, report_path, self.cfg)
idx = Indexes(self.cfg)
macsyfinder_idx = idx.find_my_indexes()
gspD_hmmer_path = self.find_data(
os.path.join('hmm', 'gspD.search_hmm.out'))
db = report._build_my_db(gspD_hmmer_path)
report._fill_my_db(macsyfinder_idx, db)
self.assertDictEqual(
db, {
'PSAE001c01_031420': (658, 73),
'PSAE001c01_051090': (714, 75),
'PSAE001c01_018920': (776, 71),
'PSAE001c01_043580': (416, 74),
'PSAE001c01_017350': (600, 70),
'PSAE001c01_013980': (759, 69),
'PSAE001c01_026600': (273, 72),
'NC_xxxxx_xx_056141': (803, 141),
'PSAE001c01_006940': (803, 68)
})
def fake_init(obj, cfg):
obj.cfg = cfg
idx = Indexes(self.cfg)
obj.sequence_idx = idx.find_my_indexes()
obj.topology_file = self.cfg.topology_file
obj._DB = {}
def fake_init(obj, cfg):
obj.cfg = cfg
idx = Indexes(self.cfg)
obj.sequence_idx = idx.find_my_indexes()
obj.topology_file = self.cfg.topology_file
obj._DB = {}
def test_find_my_indexes(self):
idx = Indexes(self.cfg)
self.assertIsNone(idx.find_my_indexes())
new_idx = os.path.join(os.path.dirname(self.cfg.sequence_db), idx.name + ".idx")
open(new_idx, 'w')
self.assertEqual(idx.find_my_indexes(), new_idx)
def test_build_force(self):
idx = Indexes(self.cfg)
idx.build(force=True)
my_idx = idx.find_my_indexes()
self.assertNotEqual(os.path.getsize(my_idx), 0)
def test_build_with_idx(self):
idx = Indexes(self.cfg)
open(os.path.join(os.path.dirname(self.cfg.sequence_db()), idx.name + ".idx"), 'w').close()
idx.build()
my_idx = idx.find_my_indexes()
self.assertEqual(os.path.getsize(my_idx), 0)
def test_build_no_idx(self):
idx = Indexes(self.cfg)
idx.build()
my_idx = idx.find_my_indexes()
self.assertEqual(my_idx, os.path.join(os.path.dirname(self.cfg.sequence_db()), idx.name + ".idx"))
