negative_phenotype_total = 0
owners = set()
studies = set()
fields_used = set()
for patient_id in patient_ids:
stderr.write(str(count) + '\r')
count += 1
owner = bot.get_owner(patient_id) or ''
study = bot.get_study(patient_id) or ''
if ((len(wanted_users) == 0 or owner.lower() in wanted_users) and
(len(wanted_studies) == 0 or study.lower() in wanted_studies)):
patient_total += 1
owners.add(owner)
studies.add(study)
patient = bot.get(patient_id)
if patient['phenotype']:
positive_phenotype_total += len(patient['phenotype'].split('|'))
if patient['negative_phenotype']:
negative_phenotype_total += len(patient['negative_phenotype'].split('|'))
for key, value in patient.items():
if value:
#print(key + ': ' + value)
fields_used.add(key)
print('Owned patients: ' + str(patient_total))
print('Average positive phenotypes per patient: ' + str(positive_phenotype_total / patient_total))
print('Average negative phenotypes per patient: ' + str(negative_phenotype_total / patient_total))
print('Owners: ' + str(len(owners)) + ', ' + str(sorted(owners)))
print('Study forms: ' + str(len(studies)) + ', ' + str(sorted(studies)))
print('Fields used at least once: ' + str(len(fields_used)) + ', ' + str(sorted(fields_used)))
patient_ids = bot.list(study, owner)
stderr.write('Looking through ' + str(len(patient_ids)) + ' patient records...\n')
stderr.write('\n')
stdout.write('#FID\tIID\tPAT\tMAT\tSEX\tPHENOTYPE\n')
writer = csv.writer(sys.stdout, delimiter='\t')
fid = study if study else '0'
for patient_id in patient_ids:
stderr.write(str(count) + '\r')
count += 1
patient = bot.get(patient_id)
iid = patient['external_id']
pat = '0'
mat = '0'
if patient.get('gender') == 'M':
sex = 1
elif patient.get('gender') == 'F':
sex = 2
else:
sex = 0
if patient.get('case_or_control') == 'case':
phenotype = 2
elif patient.get('case_or_control') == 'control':
phenotype = 1
else:
phenotype = 0
