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_bad_reader(self):
"Test that building things fails properly with a bad 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=0, 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
try:
db = SequenceFileDB(self.dbfile, reader=my_fake_reader)
try:
assert 0, "should not reach here; db construction should fail!"
finally:
db.close()
except ValueError:
pass # ValueError is expected
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_build_seqLenDict_with_bad_reader(self):
"Test that building things fails properly with a bad 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=0, 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
try:
db = SequenceFileDB(self.dbfile, reader=my_fake_reader)
try:
assert 0, "should not reach here; db construction should fail!"
finally:
db.close()
except ValueError:
pass # ValueError is expected
def test_basic_iadd(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
assert new_seq in self.db
name = (~self.db)[new_seq]
assert name == 'dnaseq.seq1', name
###
seqdb2 = SequenceFileDB(dnaseq)
try:
# Munge the filepath for testing.
seqdb2.filepath = 'foo'
new_seq2 = seqdb2['seq1']
self.db += new_seq2
name2 = (~self.db)[new_seq2]
assert name2 == 'foo.seq1', name2
finally:
seqdb2.close()
finally:
seqdb.close()
def test_basic_iadd(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
assert new_seq in self.db
name = (~self.db)[new_seq]
assert name == 'dnaseq.seq1', name
###
seqdb2 = SequenceFileDB(dnaseq)
try:
# Munge the filepath for testing.
seqdb2.filepath = 'foo'
new_seq2 = seqdb2['seq1']
self.db += new_seq2
name2 = (~self.db)[new_seq2]
assert name2 == 'foo.seq1', name2
finally:
seqdb2.close()
finally:
seqdb.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_inverse_add_behavior(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
name = (~self.db)[seq]
finally:
seqdb.close() # only need to close if exception occurs
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_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_inverse_add_behavior(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
name = (~self.db)[seq]
finally:
seqdb.close() # only need to close if exception occurs
def test_cache(self):
"Sequence slice cache mechanics."
dnaseq = testutil.datafile('dnaseq.fasta')
db = SequenceFileDB(dnaseq)
try:
# create cache components
cacheDict = {}
cacheHint = db.cacheHint
# get seq1
seq1 = db['seq1']
# _cache is only created on first cache attempt
assert not hasattr(db, '_cache')
# build an 'owner' object
class AnonymousOwner(object):
pass
owner = AnonymousOwner()
# save seq1 in cache
cacheDict['seq1'] = (seq1.start, seq1.stop)
cacheHint(cacheDict, owner)
del cacheDict # 'owner' now holds reference
# peek into _cache and assert that only the ival coordinates
# are stored
v = db._cache.values()[0]
assert len(v['seq1']) == 2
del v
# force a cache access & check that now we've stored actual string
ival = str(seq1[5:10])
v = db._cache.values()[0]
# ...check that we've stored actual string
assert len(v['seq1']) == 3
# again force cache access, this time to the stored sequence string
ival = str(seq1[5:10])
# now, eliminate all references to the cache proxy dict
del owner
# trash unused objects - not strictly necessary, because there are
# no islands of circular references & so all objects are already
# deallocated, but that's implementation dependent.
gc.collect()
# ok, cached values should now be gone.
v = db._cache.values()
assert len(v) == 0
finally:
db.close()
def test_cache(self):
"Sequence slice cache mechanics."
dnaseq = testutil.datafile('dnaseq.fasta')
db = SequenceFileDB(dnaseq)
try:
# create cache components
cacheDict = {}
cacheHint = db.cacheHint
# get seq1
seq1 = db['seq1']
# _cache is only created on first cache attempt
assert not hasattr(db, '_cache')
# build an 'owner' object
class AnonymousOwner(object):
pass
owner = AnonymousOwner()
# save seq1 in cache
cacheDict['seq1'] = (seq1.start, seq1.stop)
cacheHint(cacheDict, owner)
del cacheDict # 'owner' now holds reference
# peek into _cache and assert that only the ival coordinates
# are stored
v = db._cache.values()[0]
assert len(v['seq1']) == 2
del v
# force a cache access & check that now we've stored actual string
ival = str(seq1[5:10])
v = db._cache.values()[0]
# ...check that we've stored actual string
assert len(v['seq1']) == 3
# again force cache access, this time to the stored sequence string
ival = str(seq1[5:10])
# now, eliminate all references to the cache proxy dict
del owner
# trash unused objects - not strictly necessary, because there are
# no islands of circular references & so all objects are already
# deallocated, but that's implementation dependent.
gc.collect()
# ok, cached values should now be gone.
v = db._cache.values()
assert len(v) == 0
finally:
db.close()
def test_nlmsaslice_cache(self):
"NLMSASlice sequence caching & removal"
# set up sequences
dnaseq = testutil.datafile('dnaseq.fasta')
db = SequenceFileDB(dnaseq, autoGC=-1) # use pure WeakValueDict...
try:
gc.collect()
assert len(
db._weakValueDict) == 0, '_weakValueDict should be empty'
seq1, seq2 = db['seq1'], db['seq2']
assert len(db._weakValueDict)==2, \
'_weakValueDict should have 2 seqs'
# build referencing NLMSA
mymap = NLMSA('test', 'memory', db, pairwiseMode=True)
mymap += seq1
mymap[seq1] += seq2
mymap.build()
# check: no cache
assert not hasattr(db, '_cache'), 'should be no cache yet'
seq1, seq2 = db['seq1'], db['seq2'] # re-retrieve
# now retrieve a NLMSASlice, forcing entry of seq into cache
ival = seq1[5:10]
x = mymap[ival]
assert len(db._cache.values()) != 0
n1 = len(db._cache)
assert n1 == 1, "should be exactly one cache entry, not %d" % \
(n1, )
# ok, now trash referencing arguments & make sure of cleanup
del x
gc.collect()
assert len(db._cache.values()) == 0
n2 = len(db._cache)
assert n2 == 0, '%d objects remain; cache memory leak!' % n2
# FAIL because of __dealloc__ error in cnestedlist.NLMSASlice.
# Drop our references, the cache should empty.
del mymap, ival, seq1, seq2
gc.collect()
# check that db._weakValueDict cache is empty
assert len(
db._weakValueDict) == 0, '_weakValueDict should be empty'
finally:
db.close()
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_nlmsaslice_cache(self):
"NLMSASlice sequence caching & removal"
# set up sequences
dnaseq = testutil.datafile('dnaseq.fasta')
db = SequenceFileDB(dnaseq, autoGC=-1) # use pure WeakValueDict...
try:
gc.collect()
assert len(db._weakValueDict)==0, '_weakValueDict should be empty'
seq1, seq2 = db['seq1'], db['seq2']
assert len(db._weakValueDict)==2, \
'_weakValueDict should have 2 seqs'
# build referencing NLMSA
mymap = NLMSA('test', 'memory', db, pairwiseMode=True)
mymap += seq1
mymap[seq1] += seq2
mymap.build()
# check: no cache
assert not hasattr(db, '_cache'), 'should be no cache yet'
seq1, seq2 = db['seq1'], db['seq2'] # re-retrieve
# now retrieve a NLMSASlice, forcing entry of seq into cache
ival = seq1[5:10]
x = mymap[ival]
assert len(db._cache.values()) != 0
n1 = len(db._cache)
assert n1 == 1, "should be exactly one cache entry, not %d" % \
(n1, )
# ok, now trash referencing arguments & make sure of cleanup
del x
gc.collect()
assert len(db._cache.values()) == 0
n2 = len(db._cache)
assert n2 == 0, '%d objects remain; cache memory leak!' % n2
# FAIL because of __dealloc__ error in cnestedlist.NLMSASlice.
# Drop our references, the cache should empty.
del mymap, ival, seq1, seq2
gc.collect()
# check that db._weakValueDict cache is empty
assert len(db._weakValueDict)==0, '_weakValueDict should be empty'
finally:
db.close()
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_no_db_info(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
assert getattr(seqdb, '_persistent_id', None) is None
del seqdb.filepath
self.db += new_seq
name = (~self.db)[new_seq]
assert name == 'noname0.seq1'
finally:
seqdb.close()
def test_iadd_db_twice(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
name1 = (~self.db)[new_seq]
self.db += new_seq # should do nothing...
name2 = (~self.db)[new_seq]
assert name1 == name2 # ...leaving seq with same name.
finally:
seqdb.close()
def test_no_db_info(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
assert getattr(seqdb, '_persistent_id', None) is None
del seqdb.filepath
self.db += new_seq
name = (~self.db)[new_seq]
assert name == 'noname0.seq1'
finally:
seqdb.close()
def test_iadd_db_twice(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
name1 = (~self.db)[new_seq]
self.db += new_seq # should do nothing...
name2 = (~self.db)[new_seq]
assert name1 == name2 # ...leaving seq with same name.
finally:
seqdb.close()
def test_inverse_noadd_behavior(self):
# compare with test_inverse_add_behavior...
db = SeqPrefixUnionDict(addAll=False)
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
try:
name = (~db)[seq]
assert 0, "should not get here"
except KeyError:
pass
finally:
seqdb.close()
def test_inverse_noadd_behavior(self):
# compare with test_inverse_add_behavior...
db = SeqPrefixUnionDict(addAll=False)
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
try:
name = (~db)[seq]
assert 0, "should not get here"
except KeyError:
pass
finally:
seqdb.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 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_iadd_duplicate_seqdb(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seqdb2 = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
new_seq2 = seqdb2['seq1']
self.db += new_seq
try:
self.db += new_seq2
assert 0, "should never reach this point"
except ValueError:
pass
finally:
seqdb2.close()
finally:
seqdb.close()
def test_iadd_duplicate_seqdb(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seqdb2 = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
new_seq2 = seqdb2['seq1']
self.db += new_seq
try:
self.db += new_seq2
assert 0, "should never reach this point"
except ValueError:
pass
finally:
seqdb2.close()
finally:
seqdb.close()
class SeqPrefixUnionDict_Test(unittest.TestCase):
"""
Test SeqPrefixUnionDict.
"""
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
self.seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = SeqPrefixUnionDict({'prefix': self.seqdb})
def tearDown(self):
self.seqdb.close()
def test_basic_iadd(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
assert new_seq in self.db
name = (~self.db)[new_seq]
assert name == 'dnaseq.seq1', name
###
seqdb2 = SequenceFileDB(dnaseq)
try:
# Munge the filepath for testing.
seqdb2.filepath = 'foo'
new_seq2 = seqdb2['seq1']
self.db += new_seq2
name2 = (~self.db)[new_seq2]
assert name2 == 'foo.seq1', name2
finally:
seqdb2.close()
finally:
seqdb.close()
# NOTE, the important thing here is less the specific names that
# are given (which are based on filepath) but that different names
# are created for the various sequences when they are added.
def test_iadd_db_twice(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
name1 = (~self.db)[new_seq]
self.db += new_seq # should do nothing...
name2 = (~self.db)[new_seq]
assert name1 == name2 # ...leaving seq with same name.
finally:
seqdb.close()
def test_iadd_user_seq(self):
seq = Sequence('ATGGCAGG', 'foo')
self.db += seq
name = (~self.db)[seq]
assert name == 'user.foo' # created a new 'user' db.
# ok, make sure it doesn't wipe out the old 'user' db...
seq2 = Sequence('ATGGCAGG', 'foo2')
self.db += seq2
name = (~self.db)[seq2]
assert name == 'user.foo2'
first_name = (~self.db)[seq]
assert first_name == 'user.foo'
def test_iadd_duplicate_seqdb(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seqdb2 = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
new_seq2 = seqdb2['seq1']
self.db += new_seq
try:
self.db += new_seq2
assert 0, "should never reach this point"
except ValueError:
pass
finally:
seqdb2.close()
finally:
seqdb.close()
def test_no_db_info(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
assert getattr(seqdb, '_persistent_id', None) is None
del seqdb.filepath
self.db += new_seq
name = (~self.db)[new_seq]
assert name == 'noname0.seq1'
finally:
seqdb.close()
def test_inverse_add_behavior(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
name = (~self.db)[seq]
finally:
seqdb.close() # only need to close if exception occurs
def test_inverse_noadd_behavior(self):
# compare with test_inverse_add_behavior...
db = SeqPrefixUnionDict(addAll=False)
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
try:
name = (~db)[seq]
assert 0, "should not get here"
except KeyError:
pass
finally:
seqdb.close()
class SeqPrefixUnionDict_Test(unittest.TestCase):
"""
Test SeqPrefixUnionDict.
"""
def setUp(self):
dnaseq = testutil.datafile('dnaseq.fasta')
self.seqdb = SequenceFileDB(dnaseq) # contains 'seq1', 'seq2'
self.db = SeqPrefixUnionDict({'prefix': self.seqdb})
def tearDown(self):
self.seqdb.close()
def test_basic_iadd(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
assert new_seq in self.db
name = (~self.db)[new_seq]
assert name == 'dnaseq.seq1', name
###
seqdb2 = SequenceFileDB(dnaseq)
try:
# Munge the filepath for testing.
seqdb2.filepath = 'foo'
new_seq2 = seqdb2['seq1']
self.db += new_seq2
name2 = (~self.db)[new_seq2]
assert name2 == 'foo.seq1', name2
finally:
seqdb2.close()
finally:
seqdb.close()
# NOTE, the important thing here is less the specific names that
# are given (which are based on filepath) but that different names
# are created for the various sequences when they are added.
def test_iadd_db_twice(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
self.db += new_seq
name1 = (~self.db)[new_seq]
self.db += new_seq # should do nothing...
name2 = (~self.db)[new_seq]
assert name1 == name2 # ...leaving seq with same name.
finally:
seqdb.close()
def test_iadd_user_seq(self):
seq = Sequence('ATGGCAGG', 'foo')
self.db += seq
name = (~self.db)[seq]
assert name == 'user.foo' # created a new 'user' db.
# ok, make sure it doesn't wipe out the old 'user' db...
seq2 = Sequence('ATGGCAGG', 'foo2')
self.db += seq2
name = (~self.db)[seq2]
assert name == 'user.foo2'
first_name = (~self.db)[seq]
assert first_name == 'user.foo'
def test_iadd_duplicate_seqdb(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seqdb2 = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
new_seq2 = seqdb2['seq1']
self.db += new_seq
try:
self.db += new_seq2
assert 0, "should never reach this point"
except ValueError:
pass
finally:
seqdb2.close()
finally:
seqdb.close()
def test_no_db_info(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
new_seq = seqdb['seq1']
assert getattr(seqdb, '_persistent_id', None) is None
del seqdb.filepath
self.db += new_seq
name = (~self.db)[new_seq]
assert name == 'noname0.seq1'
finally:
seqdb.close()
def test_inverse_add_behavior(self):
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
name = (~self.db)[seq]
finally:
seqdb.close() # only need to close if exception occurs
def test_inverse_noadd_behavior(self):
# compare with test_inverse_add_behavior...
db = SeqPrefixUnionDict(addAll=False)
dnaseq = testutil.datafile('dnaseq.fasta')
seqdb = SequenceFileDB(dnaseq)
try:
seq = seqdb['seq1']
try:
name = (~db)[seq]
assert 0, "should not get here"
except KeyError:
pass
finally:
seqdb.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 Hgvs2:
def __init__(self, refseq_fn=fileconfig.FILECONFIG['REFGENE']):
""" register hg19 reference genome sequence and NCBI RefSeq transcript coordinates"""
self.genome_fn = fileconfig.FILECONFIG['REFGENOME_UCSC']
self.genome = None
if not os.path.exists(self.genome_fn):
raise IOError(
'Reference Genome Sequence (UCSC format) for %s is not found' %
self.genome_fn)
self.refseq_fn = refseq_fn
self.refseq = None
if not os.path.exists(self.refseq_fn):
raise IOError('NCBI RefSeq transcript for %s is not found' %
self.refseq_fn)
def get_transcript(self, name):
if self.refseq:
return self.refseq.get(name)
else:
raise RuntimeError(
'first, load a transcript coordinate file![%s]' %
self.refseq_fn)
def load_resource(self):
#load genome sequence
print 'loading the genome sequence [%s] for HGVS...' % self.genome_fn
self.genome = SequenceFileDB(self.genome_fn)
print 'done.'
#load refseq into dic
print 'loading the refseq transcript [%s] for HGVS...' % self.refseq_fn
fp = open(self.refseq_fn, 'r')
self.refseq = pyhgvs.utils.read_transcripts(fp)
fp.close()
print 'done.'
def close_resource(self):
self.genome.close()
self.refseq = None
def to_cDNA(self, chrom, offset, ref, alt, refseq_acc):
""" convert to HGVS nomenclature """
transcript = self.get_transcript(refseq_acc)
if not chrom.startswith('chr'):
chrom = 'chr%s' % chrom
if chrom not in CHROMOSOMES:
return None
if not chrom in self.genome.keys():
return None
cdna = pyhgvs.format_hgvs_name(chrom, offset, ref, alt, self.genome,
transcript)
if cdna:
itms = cdna.split(':')
if len(itms) > 1:
cdna = itms[1]
else:
cdna = cdna
return cdna
else:
return None
def gdna_to_vcf(self, gdna):
return pyhgvs.gdna_to_vcf(gdna, self.genome)
def to_chrom_coordinate(self, cDNA):
try:
chrom, offset, ref, alt = pyhgvs.parse_hgvs_name(cDNA, self.genome, \
get_transcript = self.get_transcript)
return chrom, offset, ref, alt
except:
print "[%s] cannot be coverted to chromosome coordinate" % cDNA
return None, None, None, None
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)
