def test_load_pcs_from_file():
pcs_dict = an.load_pcs_from_file(path.join(data_path, 'pcs.hdf5'))
assert type(pcs_dict) == dict
populations = pcs_dict['populations']
assert type(populations) == dict
assert len(populations.keys()) == 5
assert pcs_dict['pcs'].shape == (2504, 2)
def get_pcs_forplotting(platform,pc1,pc2,region='world'):
pcs = ancestry.load_pcs_from_file('%s/AN_DATA/hapmap_%s_%s_pcs.hdf5' % (settings.DATA_PATH,platform,region))
num_pop = len(pcs['populations'].keys())
header = ['PC1']
data = []
data.append(header)
for population, mask in pcs['populations'].items():
header.append(population)
pc2_ix = len(header)-1
pop_pcs = pcs['pcs'][mask]
for pc in pop_pcs:
value = [pc[0]]
value.extend([None]*(pc2_ix-1))
value.append(pc[1])
value.extend([None]*(num_pop - pc2_ix +1))
data.append(value)
header.append('YOU')
value = [None]*(num_pop+2)
value[0] = float(pc1)
value[-1] = float(pc2)
data.append(value)
return data
def get_pcs_for_population(platform,region='world',population=None):
'''Returns the PCS for a given population'''
pcs = _transform_pcs(ancestry.load_pcs_from_file('%s/AN_DATA/hapmap_%s_%s_pcs.hdf5' % (settings.DATA_PATH,platform,region)))
if population is not None:
return pcs[population]
return pcs
