def main():
global options
database = EMRDatabase(options.verbose)
database.import_data(options.emr_data_file, options.diseases_file,
options.code2disease_file)
diseases = [
"Alzheimer's disease", "Attention deficit", "Autism",
"Breast cancer (female)", "Epilepsy", "Schizophrenia"
]
D1 = "Autism"
D2 = "Epilepsy"
D3 = "Breast cancer (female)"
# Query for patients that have D1
D1_patients = database.query_emr_data(D1)
# Query for patients that have D2
D2_patients = database.query_emr_data(D2)
# Query for patients that have both D1 and D2
D1andD2_patients = database.query_emr_data([D1, D2])
# Query for patients that have either D1 or D2
D1orD2_patients = database.query_emr_data([D1, D2], OR_match=True)
# Query for patients that have D1 and not D2
D1notD2_patients = database.query_emr_data([D1, "not " + D2])
# Query for patients that have D2 and not D1
D2notD1_patients = database.query_emr_data(["not " + D1, D2])
# Query for patients that have neither D2 nor D1
noD1D2_patients = database.query_emr_data(["not " + D1, "not " + D2])
# Query for male patients with female Breast cancer
D3_male_patients = database.query_emr_data(D3, gender_filters="M")
# Query for female patients with female Breast cancer
D3_female_patients = database.query_emr_data(D3, gender_filters="F")
print "Test EMR_database queries:"
print "%-6d patients with %s" % (len(D1_patients), D1)
print "%-6d patients with %s" % (len(D2_patients), D2)
print "%-6d patients with %s and %s" % (len(D1andD2_patients), D1, D2)
print "%-6d patients with %s or %s" % (len(D1orD2_patients), D1, D2)
print "%-6d patients with %s and no %s" % (len(D1notD2_patients), D1, D2)
print "%-6d patients with %s and no %s" % (len(D2notD1_patients), D2, D1)
print "%-6d patients with no %s and no %s" % (len(noD1D2_patients), D1, D2)
print "%-6d male patients with %s" % (len(D3_male_patients), D3)
print "%-6d female patients with %s" % (len(D3_female_patients), D3)
if options.verbose:
print "Patients with %s:" % D1
for patient in D1_patients:
print "patient %s --> %s" % (patient, D1_patients[patient])
print
print "Patients with %s:" % D2
for patient in D2_patients:
print "patient %s --> %s" % (patient, D2_patients[patient])
print
print "Patients with %s and %s:" % (D1, D2)
for patient in D1andD2_patients:
print "patient %s --> %s" % (patient, D1andD2_patients[patient])
print
print "Patients with %s or %s:" % (D1, D2)
for patient in D1orD2_patients:
print "patient %s --> %s" % (patient, D1orD2_patients[patient])
print
print "Patients with %s and no %s:" % (D2, D1)
for patient in D2notD1_patients:
print "patient %s --> %s" % (patient, D2notD1_patients[patient])
print
print "Patients with %s and no %s:" % (D1, D2)
for patient in D1notD2_patients:
print "patient %s --> %s" % (patient, D1notD2_patients[patient])
print
print "Patients with no %s and no %s:" % (D1, D2)
for patient in noD1D2_patients:
print "patient %s --> %s" % (patient, noD1D2_patients[patient])
print
print "Male patients with %s:" % (D3)
for patient in D3_male_patients:
print "patient %s --> %s" % (patient, D3_male_patients[patient])
print
print "Female patients with %s:" % (D3)
for patient in D3_female_patients:
print "patient %s --> %s" % (patient, D3_female_patients[patient])
print
# Find occurrences of 6 diseases.
print
print "Occurrences of the 6 diseases:"
for n1, D1 in enumerate(diseases):
D1_patients = database.query_emr_data(D1)
print "%-6d patients with %s" % (len(D1_patients), D1)
if options.verbose:
print "Patients with %s:" % D1
for patient in D1_patients:
print "patient %s --> %s" % (patient, D1_patients[patient])
print
# Find comorbidities between the 6 diseases.
print
print "Comorbidities between the 6 diseases:"
for n1, D1 in enumerate(diseases):
for n2, D2 in enumerate(diseases):
if n1 >= n2: continue
D1andD2_patients = database.query_emr_data([D1, D2])
print("%-6d patients with %s and %s" %
(len(D1andD2_patients), D1, D2))
if options.verbose:
print "Patients with both %s and %s:" % (D1, D2)
for patient in D1andD2_patients:
print("patient %s --> %s" %
(patient, D1andD2_patients[patient]))
print
def main():
global options
database = EMRDatabase(options.verbose)
database.import_data(options.emr_data_file,
options.diseases_file,
options.code2disease_file)
diseases = ["Alzheimer's disease", "Attention deficit", "Autism",
"Breast cancer (female)", "Epilepsy", "Schizophrenia"]
D1 = "Autism"
D2 = "Epilepsy"
D3 = "Breast cancer (female)"
# Query for patients that have D1
D1_patients = database.query_emr_data(D1)
# Query for patients that have D2
D2_patients = database.query_emr_data(D2)
# Query for patients that have both D1 and D2
D1andD2_patients = database.query_emr_data([D1, D2])
# Query for patients that have either D1 or D2
D1orD2_patients = database.query_emr_data([D1, D2], OR_match = True)
# Query for patients that have D1 and not D2
D1notD2_patients = database.query_emr_data([D1, "not " + D2])
# Query for patients that have D2 and not D1
D2notD1_patients = database.query_emr_data(["not " + D1, D2])
# Query for patients that have neither D2 nor D1
noD1D2_patients = database.query_emr_data(["not " + D1, "not " + D2])
# Query for male patients with female Breast cancer
D3_male_patients = database.query_emr_data(D3 , gender_filters = "M")
# Query for female patients with female Breast cancer
D3_female_patients = database.query_emr_data(D3, gender_filters = "F")
print "Test EMR_database queries:"
print "%-6d patients with %s" %(len(D1_patients), D1)
print "%-6d patients with %s" %(len(D2_patients), D2)
print "%-6d patients with %s and %s" %(len(D1andD2_patients), D1, D2)
print "%-6d patients with %s or %s" %(len(D1orD2_patients), D1, D2)
print "%-6d patients with %s and no %s" %(len(D1notD2_patients), D1, D2)
print "%-6d patients with %s and no %s" %(len(D2notD1_patients), D2, D1)
print "%-6d patients with no %s and no %s" %(len(noD1D2_patients), D1, D2)
print "%-6d male patients with %s" %(len(D3_male_patients), D3)
print "%-6d female patients with %s" %(len(D3_female_patients), D3)
if options.verbose:
print "Patients with %s:" % D1
for patient in D1_patients:
print "patient %s --> %s" % (patient, D1_patients[patient])
print
print "Patients with %s:" % D2
for patient in D2_patients:
print "patient %s --> %s" % (patient, D2_patients[patient])
print
print "Patients with %s and %s:" % (D1, D2)
for patient in D1andD2_patients:
print "patient %s --> %s" % (patient, D1andD2_patients[patient])
print
print "Patients with %s or %s:" % (D1, D2)
for patient in D1orD2_patients:
print "patient %s --> %s" % (patient, D1orD2_patients[patient])
print
print "Patients with %s and no %s:" % (D2, D1)
for patient in D2notD1_patients:
print "patient %s --> %s" % (patient, D2notD1_patients[patient])
print
print "Patients with %s and no %s:" % (D1, D2)
for patient in D1notD2_patients:
print "patient %s --> %s" % (patient, D1notD2_patients[patient])
print
print "Patients with no %s and no %s:" % (D1, D2)
for patient in noD1D2_patients:
print "patient %s --> %s" % (patient, noD1D2_patients[patient])
print
print "Male patients with %s:" % (D3)
for patient in D3_male_patients:
print "patient %s --> %s" % (patient, D3_male_patients[patient])
print
print "Female patients with %s:" % (D3)
for patient in D3_female_patients:
print "patient %s --> %s" % (patient, D3_female_patients[patient])
print
# Find occurrences of 6 diseases.
print
print "Occurrences of the 6 diseases:"
for n1, D1 in enumerate(diseases):
D1_patients = database.query_emr_data(D1)
print "%-6d patients with %s" %(len(D1_patients), D1)
if options.verbose:
print "Patients with %s:" % D1
for patient in D1_patients:
print "patient %s --> %s" % (patient, D1_patients[patient])
print
# Find comorbidities between the 6 diseases.
print
print "Comorbidities between the 6 diseases:"
for n1, D1 in enumerate(diseases):
for n2, D2 in enumerate(diseases):
if n1 >= n2: continue
D1andD2_patients = database.query_emr_data([D1, D2])
print ("%-6d patients with %s and %s"
%(len(D1andD2_patients), D1, D2))
if options.verbose:
print "Patients with both %s and %s:" % (D1, D2)
for patient in D1andD2_patients:
print ("patient %s --> %s" % (patient,
D1andD2_patients[patient]))
print
