class ped_writer(unittest.TestCase):
def setUp(self):
self.kb = KB(driver="omero")("localhost", "root", "romeo")
def tearDown(self):
pass
def test_base(self):
def extract_data_sample(group, mset, dsample_name):
by_individual = {}
for i in self.kb.get_individuals(group):
gds = filter(lambda x: x.snpMarkersSet == mset, self.kb.get_data_samples(i, dsample_name))
assert len(gds) == 1
by_individual[i.id] = gds[0]
return by_individual
study = self.kb.get_study("TEST01")
family = self.kb.get_individuals(study)
mset = self.kb.get_snp_markers_set(label="FakeTaqSet01")
gds_by_individual = extract_data_sample(study, mset, "GenotypeDataSample")
pw = PedWriter(mset, base_path="./foo")
pw.write_map()
pw.write_family(study.id, family, gds_by_individual)
pw.close()
class ped_writer(unittest.TestCase):
def setUp(self):
self.kb = KB(driver='omero')('localhost', 'root', 'romeo')
def tearDown(self):
pass
def test_base(self):
def extract_data_sample(group, mset, dsample_name):
by_individual = {}
for i in self.kb.get_individuals(group):
gds = filter(lambda x: x.snpMarkersSet == mset,
self.kb.get_data_samples(i, dsample_name))
assert (len(gds) == 1)
by_individual[i.id] = gds[0]
return by_individual
study = self.kb.get_study('TEST01')
family = self.kb.get_individuals(study)
mset = self.kb.get_snp_markers_set(label='FakeTaqSet01')
gds_by_individual = extract_data_sample(study, mset,
'GenotypeDataSample')
pw = PedWriter(mset, base_path="./foo")
pw.write_map()
pw.write_family(study.id, family, gds_by_individual)
pw.close()
action is thought as an arrow that starts from the 'newer' object, the
GenotypeDataSample instance in this case, and has as a 'target' the
object on which the process operated. It is, essentially, a
representation of the 'inverse' of the creation process.
.. todo::
uhmmm, not sure that the Action explanation above is crystal clear :-).
"""
mset.load_markers()
kb.update_snp_positions(mset.markers, ref_genome)
data_sample_by_id = {}
family = []
for i, ind in enumerate(kb.get_individuals(study)):
family.append(ind)
action = kb.create_an_action(study, target=ind, doc='fake dataset')
conf = {'label' : 'taq-%03d' % i,
'status' : kb.DataSampleStatus.USABLE,
'action' : action,
'snpMarkersSet' : mset}
data_sample = kb.factory.create(kb.GenotypeDataSample, conf).save()
probs, conf = make_fake_data(mset)
do = kb.add_gdo_data_object(action, data_sample, probs, conf)
data_sample_by_id[ind.id] = data_sample
""" ..
Note how we first create a DataSample object (GenotypeDataSample)
which basically keeps track of the fact that there exists a genotyping
action is thought as an arrow that starts from the 'newer' object, the
GenotypeDataSample instance in this case, and has as a 'target' the
object on which the process operated. It is, essentially, a
representation of the 'inverse' of the creation process.
.. todo::
uhmmm, not sure that the Action explanation above is crystal clear :-).
"""
mset.load_markers()
kb.update_snp_positions(mset.markers, ref_genome)
data_sample_by_id = {}
family = []
for i, ind in enumerate(kb.get_individuals(study)):
family.append(ind)
action = kb.create_an_action(study, target=ind, doc='fake dataset')
conf = {
'label': 'taq-%03d' % i,
'status': kb.DataSampleStatus.USABLE,
'action': action,
'snpMarkersSet': mset
}
data_sample = kb.factory.create(kb.GenotypeDataSample, conf).save()
probs, conf = make_fake_data(mset)
do = kb.add_gdo_data_object(action, data_sample, probs, conf)
data_sample_by_id[ind.id] = data_sample
""" ..
Note how we first create a DataSample object (GenotypeDataSample)
