def parse_ped(ped_file,experiment_id):
f = open(ped_file,'r')
f.readline()
patients = []
for line in f:
line = line.strip().split(',')
p = Patient(patient_name = line[0], affliction_status=line[6]=='1', family=Family.objects.get_or_create(family_name=line[1])[0], gender= ('male' if line[5]=='0' else 'female'),experiment=Experiment.objects.get(pk=experiment_id))
patients.append(p)
Patient.objects.bulk_create(patients)
print 'Saved %s Patients in the First Pass' % len(patients)
f.close()
f = open(ped_file,'r')
f.readline()
patients = []
for line in f:
changed = False
line = line.strip().split(',')
p = Patient.objects.get(patient_name=line[0],experiment_id__exact=experiment_id)
if line[3] != '?':
changed=True
p.father = Patient.objects.get(patient_name=line[3],experiment_id__exact=experiment_id)
if line[4] != '?':
changed=True
p.mother = Patient.objects.get(patient_name=line[4],experiment_id__exact=experiment_id)
if changed:
patients.append(p)
p.save()
print 'Updated %s Patients in the Second Pass' % len(patients)
