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_find_hmmer_indexes_all_files(self):
idx = Indexes(self.cfg)
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_hmmer_indexes_all_files(self):
idx = Indexes(self.cfg)
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
new_idx = os.path.join(self.cfg.sequence_db + s)
open(new_idx, 'w')
files_2_find.append(new_idx)
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, files_2_find)
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_find_hmmer_indexes_all_files_and_virtual(self):
idx = Indexes(self.cfg)
#tester index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join("%s.%d.%s" %(self.cfg.sequence_db, i, s))
open(new_idx, 'w')
files_2_find.append(new_idx)
new_idx = os.path.join(self.cfg.sequence_db + '.pal')
open(new_idx, 'w')
files_2_find.append(new_idx)
files_2_find.sort()
hmmer_idx = idx.find_hmmer_indexes()
hmmer_idx.sort()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_hmmer_indexes_all_files_and_virtual(self):
idx = Indexes(self.cfg)
# tester index + pal
suffixes = ('.phr', '.pin', '.psd', '.psi', '.psq')
files_2_find = []
for s in suffixes:
for i in range(2):
new_idx = os.path.join("{0}.{1:d}.{2}".format(self.cfg.sequence_db, i, s))
open(new_idx, 'w')
files_2_find.append(new_idx)
new_idx = os.path.join(self.cfg.sequence_db + '.pal')
open(new_idx, 'w')
files_2_find.append(new_idx)
files_2_find.sort()
hmmer_idx = idx.find_hmmer_indexes()
hmmer_idx.sort()
self.assertListEqual(hmmer_idx, files_2_find)
def test_find_hmmer_indexes_no_files(self):
idx = Indexes(self.cfg)
#tester pas de fichier
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, [])
def test_find_hmmer_indexes_no_files(self):
idx = Indexes(self.cfg)
#tester pas de fichier
hmmer_idx = idx.find_hmmer_indexes()
self.assertListEqual(hmmer_idx, [])
