# Functions
# Script
if __name__ == '__main__':
patients = load_patients()
for pname, patient in patients.iterrows():
patient = Patient(patient)
print patient.code, patient.name
# Allele count trajectories
(inse, ind) = patient.get_insertion_trajectories('genomewide')
if not ind:
continue
inse = pd.Series(inse, name='insertion counts')
inse.index.names = ['DSI', 'position', 'insertion']
# Write to file
fn_out = get_fn_out_traj(patient.code, 'genomewide')
mkdirs(os.path.dirname(fn_out))
inse.to_pickle(fn_out)
# Sample by sample
print 'Sample by sample'
for i, sample in enumerate(patient.itersamples()):
samplename = patient.code+'_sample_'+str(i+1)
print "Sample time:", sample['days since infection'], sample.name
