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perBRENDAExtract.py
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perBRENDAExtract.py
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#
#
# perBRENDAExtract.py
#
# Date: 9/28/20
#
# PER BRENDA: Parse and Extract tool for Machine Learning applications using the BRENDA Database
#
# Gian Marco Visani1,&, Thomas McNulty1,&, and Soha Hassoun1,2,*
#
# 1 Department of Computer Science, Tufts University, 161 College Ave, Medford, MA, 02155, USA
#
# 2 Department of Chemical and Biological Engineering, Tufts University, 4 Colby St, Medford, MA, 02155, USA
#
# &Equal contribution.
#
#
from Extract import extract
import getopt, sys
import json
def main():
infile = ''
template = ''
outfile = ''
csvFile = False
compFile = False
#argument handleing
try:
optList, args = getopt.getopt(sys.argv[1:], 'hi:t:ovc', ["ifile=","templatefile=","ofile=", "csvfile=", "compoundfile="])
except getopt.GetoptError:
print('Usage: BRENDAExtract.py --ifile <inputfile> --templatefile <templatefile> --ofile <outputfile>')
sys.exit(2)
for opt, arg in optList:
if opt == '-h':
print('Usage: BRENDAExtract.py --ifile <inputfile> --templatefile <templatefile> --ofile <outputfile>')
sys.exit()
elif opt in ("-i", "--ifile"):
infile = arg
elif opt in ("-t", "--templatefile"):
template = arg
elif opt in ("-o", "--ofile"):
outfile = arg
elif opt in ("-v","--csvfile"):
csvFile = arg
elif opt in ("-c","--compoundfile"):
compFile = arg
q = extract()
input_file = open(infile).read()
input_json = json.loads(input_file)
template_file = open(template).read()
template_json = json.loads(template_file)
q.templateExtract(input_json, outfile, csvFile, compFile, template_json)
main()