ORDER BY B.person_id ASC
) B ON I.id = B.person_id
ORDER BY I.id ASC
;
""".format(utils.SUBARRAY_SEPARATOR))
print "Writing " + str(cursor.rowcount) + " files\n"
# 8 is where the batches subarray is located
subarrayPos = 8
nbBatches = utils.size_of_subarray(cursor, subarrayPos)
batchPlaceholders = utils.make_placeholders(subarrayPos, nbBatches)
headerPlaceholders = utils.make_headers("batch", 0, nbBatches)
f = cursor.fetchone()
while f:
with open(output_dir + "Individuals_" + str(f[0]) + ".tsv", "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,{0}\n".format(headerPlaceholders))
li = utils.to_prepared_list(f)
li = utils.break_subarray(li, subarrayPos, nbBatches)
file.write(("""{0},,,,{1},{2},{3},{4},{5},{6},{7},"""+batchPlaceholders+"""\n""").format(*li))
f = cursor.fetchone()
################################
### Individuals_#####_Visits ###
################################
print "Exporting Individuals Visits"
cursor.execute("""
SELECT V.person_id, V.id, V.visit_date, V.form_id, V.fasting, V.descr
FROM "public"."visit" AS V
ORDER BY V.person_id ASC, V.id ASC
;
""")
print "Writing " + str(cursor.rowcount) + " files\n"
# This section will need to create the headers and the rows dynamically because
# the number of columns is not known ahead of time! See utils.py for more info.
# 8 is where the batches subarray is located
subarrayPos = 8
nbBatches = utils.size_of_subarray(cursor, subarrayPos)
batchPlaceholders = utils.make_placeholders(subarrayPos, nbBatches)
headerPlaceholders = utils.make_headers("batch", 0, nbBatches)
f = cursor.fetchone()
current_id = -1
while f:
current_id = f[0]
os.makedirs(output_dir + str(current_id))
with open("{0}{1}/Individuals_{1}.tsv".format(output_dir, current_id), "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,{0}\n".format(headerPlaceholders))
li = utils.to_prepared_list(f)
li = utils.break_subarray(li, subarrayPos, nbBatches)
file.write(("""{0},,,,{1},{2},{3},{4},{5},{6},{7},"""+batchPlaceholders+"""\n""").format(*li))
f = cursor.fetchone()
################################
### Individuals_#####_Visits ###
################################
print "Exporting Individuals Visits"
cursor.execute("""
SELECT V.person_id, V.id, V.visit_date, V.form_id, V.fasting, V.descr
FROM "public"."visit" AS V
ORDER BY V.person_id ASC, V.id ASC
""")
print "Writing " + str(cursor.rowcount) + " files\n"
f = cursor.fetchone()
with open("{0}{1}/Individuals_{1}.tsv".format(output_dir, current_id), "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,missingCallFreq,{0}\n".format(headerPlaceholders))
familyID=utils.get_individual_info(sourcesDirectory+filename, "ID_2")
fatherID=utils.get_individual_info(sourcesDirectory+filename, "father")
motherID=utils.get_individual_info(sourcesDirectory+filename, "mother")
sex=utils.get_individual_info(sourcesDirectory+filename, "sex")
missingCallFreq=utils.get_individual_info(sourcesDirectory+filename, "missing")
migratedindividuals = migratedindividuals + 1
#According to Impute2
if sex=='1':
sex="m"
elif sex=='2':
sex="f"
li = utils.to_prepared_list(f + (familyID,fatherID,motherID,missingCallFreq))
li = utils.break_subarray(li, subarrayPos, nbBatches)
if sex != li[2]:
utils.log(logger, "Difference - Sample SEX: "+sex+ " vs. Advance SEX: "+li[2])
file.write(("""{0},{11},{12},{13},{1},{2},{3},{4},{5},{6},{7},{14},"""+batchPlaceholders+"""\n""").format(*li))
else:
os.makedirs(output_dir + str(current_id))
with open("{0}{1}/Individuals_{1}.tsv".format(output_dir, current_id), "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,missingCallFreq,{0}\n".format(headerPlaceholders))
migratedindividuals = migratedindividuals + 1
with open("{0}{1}/Individuals_{1}.tsv".format(output_dir, current_id), "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,missingCallFreq,{0}\n".format(headerPlaceholders))
familyID=utils.get_individual_info(sourcesDirectory+filename, "ID_2")
fatherID=utils.get_individual_info(sourcesDirectory+filename, "father")
motherID=utils.get_individual_info(sourcesDirectory+filename, "mother")
sex=utils.get_individual_info(sourcesDirectory+filename, "sex")
missingCallFreq=utils.get_individual_info(sourcesDirectory+filename, "missing")
migratedindividuals = migratedindividuals + 1
#According to Impute2
if sex=='1':
sex="m"
elif sex=='2':
sex="f"
li = utils.to_prepared_list(f + (familyID,fatherID,motherID,missingCallFreq))
li = utils.break_subarray(li, subarrayPos, nbBatches)
if sex != li[2]:
utils.log(logger, "Difference - Sample SEX: "+sex+ " vs. Advance SEX: "+li[2])
file.write(("""{0},{11},{12},{13},{1},{2},{3},{4},{5},{6},{7},{14},"""+batchPlaceholders+"""\n""").format(*li))
else:
os.makedirs(output_dir + str(current_id))
with open("{0}{1}/Individuals_{1}.tsv".format(output_dir, current_id), "w") as file:
file.write("individualId,familyId,paternalId,maternalId,dateOfBirth,gender,ethnicCode,centreName,region,country,notes,missingCallFreq,{0}\n".format(headerPlaceholders))
migratedindividuals = migratedindividuals + 1
li = utils.to_prepared_list(f)
