class App(object):
def __init__(self, host, user, passwd):
self.kb = KB(driver="omero")(host, user, passwd)
self.logger = logging.getLogger()
def compute(self, maker, model, release):
mset = self.kb.get_snp_markers_set(maker, model, release)
if not mset:
raise ValueError("SNPMarkersSet[%s,%s,%s] has not been defined." % (maker, model, release))
# projector = (np.arange(0, 100), np.array([101, 109]), np.arange(110,N))
# selector = kb.build_selector(
# s = self.kb.get_gdo_iterator(mset, selector, projector)
s = self.kb.get_gdo_iterator(mset)
# --
start = time.clock()
counts = algo.count_homozygotes(s)
print "counts on %d:" % counts[0], time.clock() - start
start = time.clock()
mafs = algo.maf(None, counts)
print "mafs on %d:" % counts[0], time.clock() - start
start = time.clock()
hwe = algo.hwe(None, counts)
print "hwe on %d:" % counts[0], time.clock() - start
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format' : LOG_FORMAT,
'datefmt' : LOG_DATEFMT,
'level' : log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver='omero')(args.host, args.user, args.passwd)
logger.info('Loading GenotypeDataSample objects')
dsamples = kb.get_objects(kb.GenotypeDataSample)
logger.info('Loaded %d objects' % len(dsamples))
logger.info('Loading SNPMarkersSet')
query = 'SELECT snpm FROM SNPMarkersSet snpm WHERE snpm.label = :mset_label'
mset = kb.find_all_by_query(query, {'mset_label' : args.marker_set})[0]
if not mset:
logger.error('Unable to load SNPMarkersSet with label %s' % args.marker_set)
sys.exit(2)
else:
logger.info('Object loaded')
gdo_iterator = kb.get_gdo_iterator(mset, dsamples[:args.fetch_size])
gdos = []
logger.info('Loading GDOs')
for gdo in gdo_iterator:
logger.info(gdo['vid'])
gdos.append(gdo)
logger.debug('%d/%d GDOs loaded' % (len(gdos), args.fetch_size))
logger.info('Loaded %d GDOs' % len(gdos))
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
kb = KB(driver='omero')(args.host, args.user, args.passwd)
logger.info('Loading GenotypeDataSample objects')
dsamples = kb.get_objects(kb.GenotypeDataSample)
logger.info('Loaded %d objects' % len(dsamples))
logger.info('Loading SNPMarkersSet')
query = 'SELECT snpm FROM SNPMarkersSet snpm WHERE snpm.label = :mset_label'
mset = kb.find_all_by_query(query, {'mset_label': args.marker_set})[0]
if not mset:
logger.error('Unable to load SNPMarkersSet with label %s' %
args.marker_set)
sys.exit(2)
else:
logger.info('Object loaded')
gdo_iterator = kb.get_gdo_iterator(mset, dsamples[:args.fetch_size])
gdos = []
logger.info('Loading GDOs')
for gdo in gdo_iterator:
logger.info(gdo['vid'])
gdos.append(gdo)
logger.debug('%d/%d GDOs loaded' % (len(gdos), args.fetch_size))
logger.info('Loaded %d GDOs' % len(gdos))
class App(object):
def __init__(self, host, user, passwd):
self.kb = KB(driver='omero')(host, user, passwd)
self.logger = logging.getLogger()
def compute(self, maker, model, release):
mset = self.kb.get_snp_markers_set(maker, model, release)
if not mset:
raise ValueError('SNPMarkersSet[%s,%s,%s] has not been defined.' %
(maker, model, release))
# projector = (np.arange(0, 100), np.array([101, 109]), np.arange(110,N))
# selector = kb.build_selector(
# s = self.kb.get_gdo_iterator(mset, selector, projector)
s = self.kb.get_gdo_iterator(mset)
#--
start = time.clock()
counts = algo.count_homozygotes(s)
print 'counts on %d:' % counts[0], time.clock() - start
start = time.clock()
mafs = algo.maf(None, counts)
print 'mafs on %d:' % counts[0], time.clock() - start
start = time.clock()
hwe = algo.hwe(None, counts)
print 'hwe on %d:' % counts[0], time.clock() - start
Note that what we have now is a dictionary that maps individual ids to
GenotypeDataSample objects and the latter are only handlers to get to
the actual genotyping data, not the data itself.
We can, now, do a global check on data quality.
"""
def do_check(s):
counts = algo.count_homozygotes(s)
mafs = algo.maf(None, counts)
hwe = algo.hwe(None, counts)
return mafs, hwe
gds0_data_samples = gds0_by_individual.values()
s = kb.get_gdo_iterator(mset0, data_samples=gds0_data_samples)
mafs, hwe = do_check(s)
""" ..
Similar to above, but now we subselect on a slice of the markers
"""
s = kb.get_gdo_iterator(mset0, indices=slice(1, len(mset0)-1),
data_samples=gds0_data_samples)
mafs, hwe = do_check(s)
""" ..
Same as above, but now we work on a subset of possible markers
the actual genotyping data, not the data itself.
We can, now, do a global check on data quality.
"""
def do_check(s):
counts = algo.count_homozygotes(s)
mafs = algo.maf(None, counts)
hwe = algo.hwe(None, counts)
return mafs, hwe
gds0_data_samples = gds0_by_individual.values()
s = kb.get_gdo_iterator(mset0, data_samples=gds0_data_samples)
mafs, hwe = do_check(s)
""" ..
Similar to above, but now we subselect on a slice of the markers
"""
s = kb.get_gdo_iterator(mset0,
indices=slice(1,
len(mset0) - 1),
data_samples=gds0_data_samples)
mafs, hwe = do_check(s)
""" ..
Same as above, but now we work on a subset of possible markers
class markers_set(unittest.TestCase):
def __init__(self, name):
super(markers_set, self).__init__(name)
self.kill_list = []
def setUp(self):
self.kb = KB(driver='omero')(OME_HOST, OME_USER, OME_PASSWD)
conf = {
'label': 'TEST-%f' % time.time(),
'description': 'unit test garbage',
}
self.study = self.kb.factory.create(self.kb.Study, conf).save()
self.kill_list.append(self.study)
self.action = self.kb.create_an_action(self.study)
self.kill_list.append(self.action)
def tearDown(self):
self.kill_list.reverse()
for x in self.kill_list:
self.kb.delete(x)
self.kill_list = []
def create_markers(self, N):
def marker_generator():
for i in range(N):
label = 'A%f-%d' % (time.time(), i)
yield (label, label, 'ACCA[A/B]TACCA')
source, context, release = 'unit_testing', 'markers_set', '%f' % time.time()
ref_rs_genome, dbsnp_build = 'foo-rs-genome', 123000
lvs = self.kb.create_markers(source, context, release,
ref_rs_genome, dbsnp_build,
marker_generator(), self.action)
return lvs
def create_snp_markers_set(self, lvs):
label = 'ams-%f' % time.time()
maker, model, release = 'FOO', 'FOO1', '%f' % time.time()
markers_selection = [(v[1], i, False) for i, v in enumerate(lvs)]
mset = self.kb.create_snp_markers_set(label, maker, model, release,
len(lvs),
markers_selection, self.action)
self.kill_list.append(mset)
return mset
def create_alignments(self, mset, ref_genome, n_duplicates):
mset.load_markers()
self.assertTrue(len(mset) > 0)
n_aligns = len(mset.markers) + n_duplicates
pos = []
def insert_duplicates(markers):
count = 0
for i, m in enumerate(markers):
n_copies = 1
if count < n_duplicates:
count += 1
n_copies = 2
r = (m[0], random.randint(1,26), 22 + i*1000, True,
'A' if (i%2)== 0 else 'B', n_copies)
yield r
r = (m[0], random.randint(1,26), 1 + i*1000, True,
'A' if (i%2)== 0 else 'B', n_copies)
pos.append((0,0) if n_copies > 1 else (r[1], r[2]))
yield r
aligns = [x for x in insert_duplicates(mset.markers)]
random.shuffle(aligns)
self.kb.align_snp_markers_set(mset, ref_genome, aligns, self.action)
return pos
def create_data_sample(self, mset, label):
conf = {
'label': label,
'status': self.kb.DataSampleStatus.USABLE,
'action': self.action,
'snpMarkersSet': mset,
}
data_sample = self.kb.factory.create(self.kb.GenotypeDataSample,
conf).save()
self.kill_list.append(data_sample)
return data_sample
def create_data_object(self, data_sample, add_nan=False):
probs, confs = make_fake_data(data_sample.snpMarkersSet, add_nan)
do = self.kb.add_gdo_data_object(self.action, data_sample, probs, confs)
self.kill_list.append(do)
return probs, confs
def create_aligned_mset(self, N, N_dups, ref_genome):
lvs = self.create_markers(N)
mset = self.create_snp_markers_set(lvs)
pos = self.create_alignments(mset, ref_genome, N_dups)
return mset, pos
def test_creation_destruction(self):
N = 32
lvs = self.create_markers(N)
mset = self.create_snp_markers_set(lvs)
mset.load_markers()
self.assertEqual(len(mset), N)
for lv, m in it.izip(lvs, mset.markers):
self.assertEqual(lv[1], m[0])
def test_align(self):
N = 16
N_dups = 4
ref_genome = 'g' + ('%f' % time.time())[-14:]
mset, pos = self.create_aligned_mset(N, N_dups, ref_genome)
mset.load_alignments(ref_genome)
for p, m in it.izip(pos, mset.get_markers_iterator()):
self.assertEqual(p, m.position)
def test_read_ssc(self):
N = 16
N_dups = 4
ref_genome = 'g' + ('%f' % time.time())[-14:]
mset, pos = self.create_aligned_mset(N, N_dups, ref_genome)
mset.load_markers(additional_fields=['label'])
probs, confs = make_fake_data(mset)
sample_id = 'ffoo-%f' % time.time()
fn = tempfile.NamedTemporaryFile().name
make_fake_ssc(mset, sample_id, probs, confs, fn)
probs_1, confs_1 = gio.read_ssc(fn, mset)
self.assertAlmostEqual(np.sum(np.abs(probs - probs_1)), 0.0)
self.assertAlmostEqual(np.sum(np.abs(confs - confs_1)), 0.0)
def test_gdo(self):
N = 32
lvs = self.create_markers(N)
mset = self.create_snp_markers_set(lvs)
mset.load_markers()
data_sample = self.create_data_sample(mset, 'foo-data')
probs, confs = self.create_data_object(data_sample)
probs1, confs1 = data_sample.resolve_to_data()
self.assertTrue((probs == probs1).all())
self.assertTrue((confs == confs1).all())
s = self.kb.get_gdo_iterator(mset, data_samples=[data_sample])
for i, x in enumerate(s):
self.assertTrue((probs == x['probs']).all())
self.assertTrue((confs == x['confidence']).all())
self.assertEqual(i, 0)
indices = slice(N/4, N/2)
s = self.kb.get_gdo_iterator(mset, data_samples=[data_sample],
indices=indices)
for i, x in enumerate(s):
self.assertTrue((probs[:,indices] == x['probs']).all())
self.assertTrue((confs[indices] == x['confidence']).all())
self.assertEqual(i, 0)
def test_define_range_selector(self):
N, N_dups = 16, 0
ref_genome = 'g' + ('%f' % time.time())[-14:]
mset, pos = self.create_aligned_mset(N, N_dups, ref_genome)
mset.load_alignments(ref_genome)
pos.sort()
if len(pos) > 2:
low_pos, high_pos = pos[1], pos[-2]
gc_range = (low_pos, high_pos)
range_sel = self.kb.SNPMarkersSet.define_range_selector(mset, gc_range)
i = 0
for (i, m) in enumerate(mset.get_markers_iterator()):
if i in range_sel:
self.assertTrue(low_pos <= m.position <= high_pos)
else:
self.assertTrue(low_pos > m.position or high_pos < m.position)
def test_intersect(self):
ref_genome = 'g' + ('%f' % time.time())[-14:]
N1 = 16
M1 = 2
N2 = N1/2
M2 = 1
lvs = self.create_markers(N1)
mset1 = self.create_snp_markers_set(lvs)
mset1.load_markers()
aligns = [(m[0], random.randint(1,26), 1 + i*2000, True, 'A', 1)
for i, m in enumerate(mset1.markers)]
for i in range(M1):
aligns[i] = (aligns[i][0], 0, 0, True, 'A', 0)
self.kb.align_snp_markers_set(mset1, ref_genome, aligns, self.action)
lvs = self.create_markers(N2)
mset2 = self.create_snp_markers_set(lvs)
mset2.load_markers()
aligns = [(m[0], a[1], a[2], a[3], a[4], a[5])
for m, a in it.izip(mset2.markers, aligns[:len(mset2)])]
for i in range(M2):
aligns[i] = (aligns[i][0], 0, 0, True, 'A', 0)
self.kb.align_snp_markers_set(mset2, ref_genome, aligns, self.action)
mset1.load_alignments(ref_genome)
mset2.load_alignments(ref_genome)
idx1, idx2 = self.kb.SNPMarkersSet.intersect(mset1, mset1)
self.assertTrue(np.array_equal(idx1, idx2))
self.assertEqual(len(idx1), len(mset1))
self.assertEqual(len(idx1), N1)
idx1, idx2 = self.kb.SNPMarkersSet.intersect(mset1, mset2)
self.assertEqual(len(idx1), len(idx2))
self.assertEqual(len(idx1), N2 - max(M1, M2))
for i,j in it.izip(idx1, idx2):
m1, m2 = mset1[i], mset2[j]
self.assertEqual(m1.position, m2.position)
self.assertTrue(m1.position > (0,0))
def test_speed(self):
ref_genome = 'g' + ('%f' % time.time())[-14:]
N1 = 1024*1024
N2 = N1/2
beg = time.time()
lvs = self.create_markers(N1)
print ''
print 'creating %d markers took %f' % (N1, time.time() - beg)
beg = time.time()
mset1 = self.create_snp_markers_set(lvs)
print 'creating a markers set with %d markers took %f' % (N1,
time.time() - beg)
beg = time.time()
mset1.load_markers()
print 'loading markers took %f' % (time.time() - beg)
beg = time.time()
aligns = [(m[0], random.randint(1,26), 1 + i*2000, True, 'A', 1)
for i, m in enumerate(mset1.markers)]
print 'creating %d aligns took %f' % (N1, time.time() - beg)
beg = time.time()
self.kb.align_snp_markers_set(mset1, ref_genome, aligns, self.action)
print 'saving %d aligns took %f' % (N1, time.time() - beg)
beg = time.time()
mset1.load_alignments(ref_genome)
print 'loading %d aligns took %f' % (N1, time.time() - beg)
beg = time.time()
idx1, idx2 = self.kb.SNPMarkersSet.intersect(mset1, mset1)
print 'intersecting %d aligns took %f' % (N1, time.time() - beg)
def test_speed_gdo(self):
N = 934968
beg = time.time()
lvs = self.create_markers(N)
print ''
print 'creating %d markers took %f' % (N, time.time() - beg)
mset = self.create_snp_markers_set(lvs)
beg = time.time()
mset.load_markers()
print 'loading %d markers took %f' % (N, time.time() - beg)
beg = time.time()
data_sample = self.create_data_sample(mset, 'foo-data')
print 'creating a data sample took %f' % (time.time() - beg)
beg = time.time()
probs, confs = self.create_data_object(data_sample)
print 'creating a data object took %f' % (time.time() - beg)
beg = time.time()
probs1, confs1 = data_sample.resolve_to_data()
print 'resolving to data took %f' % (time.time() - beg)
self.assertTrue((probs == probs1).all())
self.assertTrue((confs == confs1).all())
beg = time.time()
s = self.kb.get_gdo_iterator(mset, data_samples=[data_sample])
for i, x in enumerate(s):
self.assertTrue((probs == x['probs']).all())
self.assertTrue((confs == x['confidence']).all())
self.assertEqual(i, 0)
print 'iterating took %f' % (time.time() - beg)
indices = slice(N/4, N/2)
beg = time.time()
s = self.kb.get_gdo_iterator(mset, data_samples=[data_sample],
indices=indices)
for i, x in enumerate(s):
self.assertTrue((probs[:,indices] == x['probs']).all())
self.assertTrue((confs[indices] == x['confidence']).all())
self.assertEqual(i, 0)
print 'iterating with indices took %f' % (time.time() - beg)