class PrefixUnionDict_Test(unittest.TestCase):
"""
Test for all of the basic dictionary functions on 'PrefixUnionDict'.
"""
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
def tearDown(self):
close_pud_dicts(self.db)
def test_keys(self):
"PrefixUnionDict keys"
k = self.db.keys()
k.sort()
assert k == ['prefix.seq1', 'prefix.seq2']
def test_contains(self):
"PrefixUnionDict contains"
# first, check "is this sequence name in the PUD?"-style contains.
assert 'prefix.seq1' in self.db
assert 'prefix.seq2' in self.db
assert 'foo' not in self.db
assert 'prefix.foo' not in self.db
# now, check "is this sequence in the PUD?"
seq = self.db['prefix.seq1']
assert seq in self.db
# finally, check failure: "is something other than str/seq in db"
try:
12345 in self.db
assert 0, "should not get to this point"
except AttributeError:
pass
def test_invert_class(self):
"PrefixUnionDict __invert__"
seq = self.db['prefix.seq1']
inversedb = ~self.db
assert inversedb[seq] == 'prefix.seq1'
assert seq in inversedb
assert 'foo' not in inversedb
def test_funny_key(self):
"check handling of ID containing multiple separators"
dnaseq = testutil.datafile('funnyseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
try:
pudb = PrefixUnionDict({'prefix': seqdb})
seq = pudb['prefix.seq.1.more']
finally:
seqdb.close()
def test_funny_key2(self):
"check handling of ID containing multiple separators"
dnaseq = testutil.datafile('funnyseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
try:
pudb = PrefixUnionDict({'prefix': seqdb})
seq = pudb['prefix.seq.2.even.longer']
finally:
seqdb.close()
def test_has_key(self):
"PrefixUnionDict has key"
assert 'prefix.seq1' in self.db
assert 'prefix.seq2' in self.db
assert 'prefix.foo' not in self.db
assert 'foo' not in self.db
def test_get(self):
"PrefixUnionDict get"
assert self.db.get('foo') is None
assert self.db.get('prefix.foo') is None
assert self.db.get('prefix.seq1') is not None
assert str(self.db.get('prefix.seq1')).startswith('atggtgtca')
assert self.db.get('prefix.seq2') is not None
assert str(self.db.get('prefix.seq2')).startswith('GTGTTGAA')
assert self.db.get('foo.bar') is None
assert self.db.get(12345) is None
def test_get_prefix_id(self):
try:
self.db.get_prefix_id(12345)
assert 0, "should not get here"
except KeyError:
pass
def test_getName(self):
seq1 = self.db['prefix.seq1']
name = self.db.getName(seq1)
assert name == 'prefix.seq1'
def test_items(self):
"PrefixUnionDict items"
i = [k for (k, v) in self.db.items()]
i.sort()
assert i == ['prefix.seq1', 'prefix.seq2']
def test_iterkeys(self):
"PrefixUnionDict iterkeys"
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def test_itervalues(self):
"PrefixUnionDict itervalues"
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv == iv
def test_iteritems(self):
"PrefixUnionDict iteritems"
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii
# test some things other than dict behavior
def test_keyerror(self):
"PrefixUnionDict keyerror"
"Make sure that the PrefixUnionDict KeyError is informative."
try:
self.db['prefix.foo']
except KeyError, e:
assert "no key 'foo' in " in str(e), str(e)
try:
self.db['foo']
except KeyError, e:
assert "invalid id format; no prefix: foo" in str(e), str(e)
class PrefixUnionDict_Test(unittest.TestCase):
"""
Test for all of the basic dictionary functions on 'PrefixUnionDict'.
"""
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
def tearDown(self):
close_pud_dicts(self.db)
def test_keys(self):
"PrefixUnionDict keys"
k = self.db.keys()
k.sort()
assert k == ['prefix.seq1', 'prefix.seq2']
def test_contains(self):
"PrefixUnionDict contains"
# first, check "is this sequence name in the PUD?"-style contains.
assert 'prefix.seq1' in self.db
assert 'prefix.seq2' in self.db
assert 'foo' not in self.db
assert 'prefix.foo' not in self.db
# now, check "is this sequence in the PUD?"
seq = self.db['prefix.seq1']
assert seq in self.db
# finally, check failure: "is something other than str/seq in db"
try:
12345 in self.db
assert 0, "should not get to this point"
except AttributeError:
pass
def test_invert_class(self):
"PrefixUnionDict __invert__"
seq = self.db['prefix.seq1']
inversedb = ~self.db
assert inversedb[seq] == 'prefix.seq1'
assert seq in inversedb
assert 'foo' not in inversedb
def test_funny_key(self):
"check handling of ID containing multiple separators"
dnaseq = testutil.datafile('funnyseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
try:
pudb = PrefixUnionDict({'prefix': seqdb})
seq = pudb['prefix.seq.1.more']
finally:
seqdb.close()
def test_funny_key2(self):
"check handling of ID containing multiple separators"
dnaseq = testutil.datafile('funnyseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
try:
pudb = PrefixUnionDict({'prefix': seqdb})
seq = pudb['prefix.seq.2.even.longer']
finally:
seqdb.close()
def test_has_key(self):
"PrefixUnionDict has key"
assert 'prefix.seq1' in self.db
assert 'prefix.seq2' in self.db
assert 'prefix.foo' not in self.db
assert 'foo' not in self.db
def test_get(self):
"PrefixUnionDict get"
assert self.db.get('foo') is None
assert self.db.get('prefix.foo') is None
assert self.db.get('prefix.seq1') is not None
assert str(self.db.get('prefix.seq1')).startswith('atggtgtca')
assert self.db.get('prefix.seq2') is not None
assert str(self.db.get('prefix.seq2')).startswith('GTGTTGAA')
assert self.db.get('foo.bar') is None
assert self.db.get(12345) is None
def test_get_prefix_id(self):
try:
self.db.get_prefix_id(12345)
assert 0, "should not get here"
except KeyError:
pass
def test_getName(self):
seq1 = self.db['prefix.seq1']
name = self.db.getName(seq1)
assert name == 'prefix.seq1'
def test_items(self):
"PrefixUnionDict items"
i = [k for (k, v) in self.db.items()]
i.sort()
assert i == ['prefix.seq1', 'prefix.seq2']
def test_iterkeys(self):
"PrefixUnionDict iterkeys"
kk = self.db.keys()
kk.sort()
ik = list(self.db.iterkeys())
ik.sort()
assert kk == ik
def test_itervalues(self):
"PrefixUnionDict itervalues"
kv = self.db.values()
kv.sort()
iv = list(self.db.itervalues())
iv.sort()
assert kv == iv
def test_iteritems(self):
"PrefixUnionDict iteritems"
ki = self.db.items()
ki.sort()
ii = list(self.db.iteritems())
ii.sort()
assert ki == ii
# test some things other than dict behavior
def test_keyerror(self):
"PrefixUnionDict keyerror"
"Make sure that the PrefixUnionDict KeyError is informative."
try:
self.db['prefix.foo']
except KeyError, e:
assert "no key 'foo' in " in str(e), str(e)
try:
self.db['foo']
except KeyError, e:
assert "invalid id format; no prefix: foo" in str(e), str(e)
