individuals. To register this dependency and how the dependency was
established, each DataSample object is linked with an action to the
the relevant Individual instance. Mainly for historical reasons, the
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
""" ..
individuals. To register this dependency and how the dependency was
established, each DataSample object is linked with an action to the
the relevant Individual instance. Mainly for historical reasons, the
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