def test_build_seqLenDict_with_reader(self):
"Test that building things works properly when specifying a reader."
class InfoBag(object):
def __init__(self, **kw):
self.__dict__.update(kw)
# first, load the db & save the sequence info in a list
l = []
db = SequenceFileDB(self.dbfile)
try:
for k, v in db.items():
info = InfoBag(id=k, length=len(v), sequence=str(v))
l.append(info)
finally:
# now, erase the existing files, and recreate the db.
db.close()
self.trash_intermediate_files()
# create a fake reader with access to the saved info
def my_fake_reader(fp, filename, info_list=l):
return info_list
# now try creating with the fake reader
db = SequenceFileDB(self.dbfile, reader=my_fake_reader)
# did it work?
try:
assert str(db.get('seq1')).startswith('atggtgtca')
assert str(db.get('seq2')).startswith('GTGTTGAA')
finally:
db.close()
def test_basic_construction(self):
db = SequenceFileDB(self.dbfile)
try:
assert str(db.get('seq1')).startswith('atggtgtca')
assert str(db.get('seq2')).startswith('GTGTTGAA')
finally:
db.close()
def test_build_seqLenDict_with_reader(self):
"Test that building things works properly when specifying a reader."
class InfoBag(object):
def __init__(self, **kw):
self.__dict__.update(kw)
# first, load the db & save the sequence info in a list
l = []
db = SequenceFileDB(self.dbfile)
try:
for k, v in db.items():
info = InfoBag(id=k, length=len(v), sequence=str(v))
l.append(info)
finally:
# now, erase the existing files, and recreate the db.
db.close()
self.trash_intermediate_files()
# create a fake reader with access to the saved info
def my_fake_reader(fp, filename, info_list=l):
return info_list
# now try creating with the fake reader
db = SequenceFileDB(self.dbfile, reader=my_fake_reader)
# did it work?
try:
assert str(db.get('seq1')).startswith('atggtgtca')
assert str(db.get('seq2')).startswith('GTGTTGAA')
finally:
db.close()
def test_basic_construction(self):
db = SequenceFileDB(self.dbfile)
try:
assert str(db.get('seq1')).startswith('atggtgtca')
assert str(db.get('seq2')).startswith('GTGTTGAA')
finally:
db.close()
class SequenceFileDB_Test(unittest.TestCase):
"""
Test for all of the basic dictionary functions on 'SequenceFileDB',
among other things.
"""
def setUp(self):
"Test setup"
dnaseq = testutil.datafile('dnaseq.fasta')
self.db = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db._weakValueDict.clear() # clear the cache
def tearDown(self):
self.db.close() # must close SequenceFileDB!
def test_len(self):
assert len(self.db) == 2
def test_seqInfoDict_len(self):
assert len(self.db.seqInfoDict) == 2
def test_no_file_given(self):
"Make sure that a TypeError is raised when no file is available"
try:
db = SequenceFileDB()
assert 0, "should not reach this point"
except TypeError:
pass
def test_seq_descriptor(self):
"Check the '.seq' attribute (tied to a descriptor)"
s = self.db['seq1']
assert str(s) == str(s.seq)
def test_cache(self):
"SequenceDB cache test"
assert len(self.db._weakValueDict) == 0
seq1 = self.db['seq1']
# cache populated?
assert len(self.db._weakValueDict) == 1
assert 'seq1' in self.db._weakValueDict
# cache functions?
seq1_try2 = self.db['seq1']
assert seq1 is seq1_try2
def test_clear_cache(self):
"SequenceDB clear_cache test"
assert len(self.db._weakValueDict) == 0
seq1 = self.db['seq1']
# cache populated?
assert len(self.db._weakValueDict) == 1
assert 'seq1' in self.db._weakValueDict
# clear_cache functions?
self.db.clear_cache()
seq1_try3 = self.db['seq1']
assert seq1 is not seq1_try3
def test_keys(self):
"SequenceFileDB keys"
k = self.db.keys()
k.sort()
assert k == ['seq1', 'seq2']
def test_contains(self):
"SequenceFileDB contains"
assert 'seq1' in self.db, self.db.keys()
assert 'seq2' in self.db
assert 'foo' not in self.db
def test_invert_class(self):
"SequenceFileDB __invert__"
seq = self.db['seq1']
inversedb = ~self.db
assert inversedb[seq] == 'seq1'
assert seq in inversedb
assert 'foo' not in inversedb
def test_keys_info(self):
"SequenceFileDB keys info"
k = self.db.seqInfoDict.keys()
k.sort()
assert k == ['seq1', 'seq2']
def test_contains_info(self):
"SequenceFileDB contains info"
assert 'seq1' in self.db.seqInfoDict
assert 'seq2' in self.db.seqInfoDict
assert 'foo' not in self.db.seqInfoDict
def test_has_key(self):
"SequenceFileDB has key"
assert 'seq1' in self.db
assert 'seq2' in self.db
assert 'foo' not in self.db
def test_get(self):
"SequenceFileDB get"
assert self.db.get('foo') is None
assert self.db.get('seq1') is not None
assert str(self.db.get('seq1')).startswith('atggtgtca')
assert self.db.get('seq2') is not None
assert str(self.db.get('seq2')).startswith('GTGTTGAA')
def test_items(self):
"SequenceFileDB items"
i = [k for (k, v) in self.db.items()]
i.sort()
assert i == ['seq1', 'seq2']
def test_iterkeys(self):
"SequenceFileDB iterkeys"
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def test_itervalues(self):
"SequenceFileDB itervalues"
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv == iv
def test_iteritems(self):
"SequenceFileDB iteritems"
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii
def test_readonly(self):
"SequenceFileDB readonly"
try:
self.db.copy() # what should 'copy' do on SequenceFileDB?
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.clear()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.setdefault('foo')
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.pop()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.popitem()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.update({})
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
# test some things other than dict behavior
def test_keyerror(self):
"""SequenceFileDB keyerror.
Make sure that the SequenceFileDB KeyError is informative."""
try:
self.db['foo']
except KeyError, e:
assert "no key 'foo' in database <SequenceFileDB" in str(e), str(e)
class SequenceFileDB_Test(object):
"""
Test for all of the basic dictionary functions on 'SequenceFileDB'.
"""
def setup(self):
self.db = SequenceFileDB('dnaseq') # contains 'seq1', 'seq2'
def keys_test(self):
k = self.db.keys()
k.sort()
assert k == ['seq1', 'seq2']
def contains_test(self):
assert 'seq1' in self.db, self.db.keys()
assert 'seq2' in self.db
assert 'foo' not in self.db
def keys_info_test(self):
k = self.db.seqInfoDict.keys()
k.sort()
assert k == ['seq1', 'seq2']
def contains_info_test(self):
assert 'seq1' in self.db.seqInfoDict
assert 'seq2' in self.db.seqInfoDict
assert 'foo' not in self.db.seqInfoDict
def has_key_test(self):
assert self.db.has_key('seq1')
assert self.db.has_key('seq2')
assert not self.db.has_key('foo')
def get_test(self):
assert self.db.get('foo') is None
assert self.db.get('seq1') is not None
assert str(self.db.get('seq1')).startswith('atggtgtca')
assert self.db.get('seq2') is not None
assert str(self.db.get('seq2')).startswith('GTGTTGAA')
def items_test(self):
i = [ k for (k,v) in self.db.items() ]
i.sort()
assert i == ['seq1', 'seq2']
def iterkeys_test(self):
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def itervalues_test(self):
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv == iv
def iteritems_test(self):
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii
def readonly_test(self):
try:
self.db.copy() # what should 'copy' do on SequenceFileDB?
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.clear()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.setdefault('foo')
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.pop()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.popitem()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.update({})
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
# test some things other than dict behavior
def keyerror_test(self):
"Make sure that the SequenceFileDB KeyError is informative."
try:
self.db['foo']
except KeyError, e:
assert "no key 'foo' in database <SequenceFileDB" in str(e), str(e)
class SequenceFileDB_Test(unittest.TestCase):
"""
Test for all of the basic dictionary functions on 'SequenceFileDB',
among other things.
"""
def setUp(self):
"Test setup"
dnaseq = testutil.datafile('dnaseq.fasta')
self.db = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db._weakValueDict.clear() # clear the cache
def tearDown(self):
self.db.close() # must close SequenceFileDB!
def test_len(self):
assert len(self.db) == 2
def test_seqInfoDict_len(self):
assert len(self.db.seqInfoDict) == 2
def test_no_file_given(self):
"Make sure that a TypeError is raised when no file is available"
try:
db = SequenceFileDB()
assert 0, "should not reach this point"
except TypeError:
pass
def test_seq_descriptor(self):
"Check the '.seq' attribute (tied to a descriptor)"
s = self.db['seq1']
assert str(s) == str(s.seq)
def test_cache(self):
"SequenceDB cache test"
assert len(self.db._weakValueDict) == 0
seq1 = self.db['seq1']
# cache populated?
assert len(self.db._weakValueDict) == 1
assert 'seq1' in self.db._weakValueDict
# cache functions?
seq1_try2 = self.db['seq1']
assert seq1 is seq1_try2
def test_clear_cache(self):
"SequenceDB clear_cache test"
assert len(self.db._weakValueDict) == 0
seq1 = self.db['seq1']
# cache populated?
assert len(self.db._weakValueDict) == 1
assert 'seq1' in self.db._weakValueDict
# clear_cache functions?
self.db.clear_cache()
seq1_try3 = self.db['seq1']
assert seq1 is not seq1_try3
def test_keys(self):
"SequenceFileDB keys"
k = self.db.keys()
k.sort()
assert k == ['seq1', 'seq2']
def test_contains(self):
"SequenceFileDB contains"
assert 'seq1' in self.db, self.db.keys()
assert 'seq2' in self.db
assert 'foo' not in self.db
def test_invert_class(self):
"SequenceFileDB __invert__"
seq = self.db['seq1']
inversedb = ~self.db
assert inversedb[seq] == 'seq1'
assert seq in inversedb
assert 'foo' not in inversedb
def test_keys_info(self):
"SequenceFileDB keys info"
k = self.db.seqInfoDict.keys()
k.sort()
assert k == ['seq1', 'seq2']
def test_contains_info(self):
"SequenceFileDB contains info"
assert 'seq1' in self.db.seqInfoDict
assert 'seq2' in self.db.seqInfoDict
assert 'foo' not in self.db.seqInfoDict
def test_has_key(self):
"SequenceFileDB has key"
assert 'seq1' in self.db
assert 'seq2' in self.db
assert 'foo' not in self.db
def test_get(self):
"SequenceFileDB get"
assert self.db.get('foo') is None
assert self.db.get('seq1') is not None
assert str(self.db.get('seq1')).startswith('atggtgtca')
assert self.db.get('seq2') is not None
assert str(self.db.get('seq2')).startswith('GTGTTGAA')
def test_items(self):
"SequenceFileDB items"
i = [k for (k, v) in self.db.items()]
i.sort()
assert i == ['seq1', 'seq2']
def test_iterkeys(self):
"SequenceFileDB iterkeys"
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def test_itervalues(self):
"SequenceFileDB itervalues"
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv == iv
def test_iteritems(self):
"SequenceFileDB iteritems"
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii
def test_readonly(self):
"SequenceFileDB readonly"
try:
self.db.copy() # what should 'copy' do on SequenceFileDB?
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.clear()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.setdefault('foo')
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.pop()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.popitem()
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
try:
self.db.update({})
assert 0, 'this method should raise NotImplementedError'
except NotImplementedError:
pass
# test some things other than dict behavior
def test_keyerror(self):
"""SequenceFileDB keyerror.
Make sure that the SequenceFileDB KeyError is informative."""
try:
self.db['foo']
except KeyError, e:
assert "no key 'foo' in database <SequenceFileDB" in str(e), str(e)