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)
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_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_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()
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 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
