def test_headerfile_write_fail(self):
subdb = SequenceFileDB(self.dbfile)
try:
del subdb.filepath # remove 'filepath' attribute for test
db = PrefixUnionDict({'prefix': subdb})
assert len(db) == 2
assert 'prefix.seq1' in db
output = testutil.tempdatafile('prefixUnionDict-write-fail.txt')
try:
db.writeHeaderFile(output)
except AttributeError:
pass
finally:
subdb.close() # closes both db and subdb
def test_headerfile_write_fail(self):
subdb = SequenceFileDB(self.dbfile)
try:
del subdb.filepath # remove 'filepath' attribute for test
db = PrefixUnionDict({'prefix': subdb})
assert len(db) == 2
assert 'prefix.seq1' in db
output = testutil.tempdatafile('prefixUnionDict-write-fail.txt')
try:
db.writeHeaderFile(output)
except AttributeError:
pass
finally:
subdb.close() # closes both db and subdb
def test_headerfile_create(self):
header = testutil.datafile('prefixUnionDict-1.txt')
db = PrefixUnionDict(filename=header)
try:
assert len(db) == 2
assert 'a.seq1' in db
finally:
close_pud_dicts(db)
def test_headerfile_create_with_trypath(self):
header = testutil.datafile('prefixUnionDict-1.txt')
db = PrefixUnionDict(filename=header,
trypath=[os.path.dirname(header)])
try:
assert len(db) == 2, db.prefixDict
finally:
close_pud_dicts(db)
class PrefixUnionMemberDict_Test(unittest.TestCase):
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
self.mdb = self.db.newMemberDict()
def tearDown(self):
close_pud_dicts(self.db)
def test_basic(self):
self.mdb['prefix'] = 'this is from seqdb dnaseq.fasta'
seq = self.db['prefix.seq1']
assert self.mdb[seq] == 'this is from seqdb dnaseq.fasta'
def test_possible_keys(self):
assert list(self.mdb.possibleKeys()) == ['prefix']
def test_bad_prefix(self):
try:
self.mdb['foo'] = "xyz"
assert 0, "should fail before this"
except KeyError:
pass
def test_bad_keytype(self):
try:
self.mdb['some non-seq-obj']
assert 0, "should fail before this"
except TypeError:
pass
def test_default_val(self):
self.mdb = self.db.newMemberDict(default='baz')
seq = self.db['prefix.seq1']
assert self.mdb[seq] == 'baz'
def test_no_default_val(self):
self.mdb = self.db.newMemberDict()
seq = self.db['prefix.seq1']
try:
self.mdb[seq]
assert 0, "should fail before this"
except KeyError:
pass
class PrefixUnionMemberDict_Test(unittest.TestCase):
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
self.mdb = self.db.newMemberDict()
def tearDown(self):
close_pud_dicts(self.db)
def test_basic(self):
self.mdb['prefix'] = 'this is from seqdb dnaseq.fasta'
seq = self.db['prefix.seq1']
assert self.mdb[seq] == 'this is from seqdb dnaseq.fasta'
def test_possible_keys(self):
assert list(self.mdb.possibleKeys()) == ['prefix']
def test_bad_prefix(self):
try:
self.mdb['foo'] = "xyz"
assert 0, "should fail before this"
except KeyError:
pass
def test_bad_keytype(self):
try:
self.mdb['some non-seq-obj']
assert 0, "should fail before this"
except TypeError:
pass
def test_default_val(self):
self.mdb = self.db.newMemberDict(default='baz')
seq = self.db['prefix.seq1']
assert self.mdb[seq] == 'baz'
def test_no_default_val(self):
self.mdb = self.db.newMemberDict()
seq = self.db['prefix.seq1']
try:
self.mdb[seq]
assert 0, "should fail before this"
except KeyError:
pass
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_headerfile_create_fail(self):
header = testutil.datafile('prefixUnionDict-3.txt')
try:
db = PrefixUnionDict(filename=header)
assert 0, "should not reach this point"
except IOError:
pass
except AssertionError:
close_pud_dicts(db)
raise
def test_headerfile_write(self):
header = testutil.datafile('prefixUnionDict-2.txt')
db = PrefixUnionDict(filename=header)
try:
assert len(db) == 4
assert 'a.seq1' in db
assert 'b.seq1' in db
output = testutil.tempdatafile('prefixUnionDict-write.txt')
db.writeHeaderFile(output)
finally:
close_pud_dicts(db)
db2 = PrefixUnionDict(filename=output,
trypath=[os.path.dirname(header)])
try:
assert len(db2) == 4
assert 'a.seq1' in db2
assert 'b.seq1' in db2
finally:
close_pud_dicts(db2)
def test_headerfile_write(self):
header = testutil.datafile('prefixUnionDict-2.txt')
db = PrefixUnionDict(filename=header)
try:
assert len(db) == 4
assert 'a.seq1' in db
assert 'b.seq1' in db
output = testutil.tempdatafile('prefixUnionDict-write.txt')
db.writeHeaderFile(output)
finally:
close_pud_dicts(db)
db2 = PrefixUnionDict(filename=output,
trypath=[os.path.dirname(header)])
try:
assert len(db2) == 4
assert 'a.seq1' in db2
assert 'b.seq1' in db2
finally:
close_pud_dicts(db2)
def test_headerfile_create_conflict(self):
"test non-empty prefixDict with a passed in PUD header file: conflict"
subdb = SequenceFileDB(self.dbfile)
try:
header = testutil.datafile('prefixUnionDict-1.txt')
try:
db = PrefixUnionDict(filename=header,
prefixDict={'foo': subdb})
assert 0, "should not get here"
except TypeError:
pass
finally:
subdb.close()
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)
def setup(self):
blastdb = SequenceFileDB('dnaseq') # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({ 'prefix' : blastdb })
class PrefixUnionDict_Test(object):
"""
Test for all of the basic dictionary functions on 'PrefixUnionDict'.
"""
def setup(self):
blastdb = SequenceFileDB('dnaseq') # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({ 'prefix' : blastdb })
def keys_test(self):
k = self.db.keys()
k.sort()
assert k == ['prefix.seq1', 'prefix.seq2']
def contains_test(self):
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
def has_key_test(self):
assert self.db.has_key('prefix.seq1')
assert self.db.has_key('prefix.seq2')
assert not self.db.has_key('prefix.foo')
assert not self.db.has_key('foo')
def get_test(self):
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')
def items_test(self):
i = [ k for (k,v) in self.db.items() ]
i.sort()
assert i == ['prefix.seq1', 'prefix.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
# test some things other than dict behavior
def keyerror_test(self):
"Make sure that the PrefixUnionDict KeyError is informative."
try:
self.db['prefix.foo']
except KeyError, e:
assert "no key 'prefix.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)
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
self.mdb = self.db.newMemberDict()
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)
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = PrefixUnionDict({'prefix': seqdb})
self.mdb = self.db.newMemberDict()
def test_empty_create(self):
db = PrefixUnionDict()
assert len(db) == 0
