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flattening_pr.py
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flattening_pr.py
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import sys
import datetime
def notNA(s):
return s != 'NA' and s != ''
# read the input file the first pass to identify valid prcodes
fin = open(sys.argv[1], 'r')
line = fin.readline().strip('\n').replace('"', '')
items = line.split(',')
# read column names from csv
col = dict()
for i in range(len(items)):
# be careful to the input csv. if it contains the empty first column, column number has to be i
# if it does not contain empty first column, the column number is i + 1
col[items[i]] = i;
# read data and identify valid prcodes
prcols = [pair[1] for pair in col.items() if pair[0].find('oproc') >= 0 or pair[0] == 'proc_p']
validPrCodes = set()
count = 0
while (True):
count = count + 1
if (count % 100000 == 0):
print('Identifying valid prCodes ' + str(count) + 'row')
line = fin.readline()
if not line:
break
items = line.strip('\n').split(',')
# find pr codes for this admission
for colnum in prcols:
if notNA(items[colnum]):
validPrCodes.add(int(items[colnum]))
fin.close()
# valid pr codes identified
validPrCodes = list(validPrCodes)
validPrCodes.sort()
print('These prccs codes are valid:' + str(validPrCodes))
# add PRCCS columns to col
for i in validPrCodes:
count = count + 1
col['PRCCS_' + str(i)] = max(col.values()) + 1
# write column names to output file
fout = open(sys.argv[2], 'w')
items = list(col.items())
items.sort(key = lambda item: item[1])
fout.write(','.join([item[0] for item in items]) + '\n')
print("start flattening ", datetime.datetime.now())
# read the input file 2nd pass to append flattened PRCCS columns
fin = open(sys.argv[1], 'r')
line = fin.readline().strip('\n').replace('"', '')
count = 0
while (True):
count = count + 1
if (count % 100000 == 0):
print('Flattening ' + str(count) + 'row')
line = fin.readline()
if not line:
break
newline = line.strip('\n')
items = newline.split(',')
# Add PRCCS values
prCodes = [int(items[colnum]) for colnum in prcols if notNA(items[colnum])];
for i in validPrCodes:
if i in prCodes:
newline += ',1'
else:
newline += ',0'
dummy=fout.write(newline + '\n')
print("end. ", datetime.datetime.now())
fin.close()
fout.close()