parser.add_argument('--show-status', help='show details on reactions with different status', action='store_true', dest='showStatus', default=False)
parser.add_argument('--show-stoich', help='show details on reactions with different stoichiometry', action='store_true', dest='showStoich', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# The --show-details option turns on all of the detail options.
if args.showDetails:
args.showNames = True
args.showStatus = True
args.showStoich = True
# Read the reactions from the first file.
helper = BiochemHelper()
firstReactions = helper.buildDictFromListOfObjects(helper.readReactionsFile(args.rxnfile1))
print 'First reaction file: %s' %(args.rxnfile1)
print ' Number of reactions: %d' %(len(firstReactions))
# Read the compounds from the second file.
secondReactions = helper.buildDictFromListOfObjects(helper.readReactionsFile(args.rxnfile2))
print 'Second reaction file: %s' %(args.rxnfile2)
print ' Number of reactions: %d' %(len(secondReactions))
# Track differences in reactions.
reactionsOnlyInFirst = list()
reactionsOnlyInSecond = list()
diffNames = set()
diffStatus = set()
diffStoich = set()
different = set()
dest='flatFile',
default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# The --show-details option turns on all of the detail options.
if args.showDetails:
args.showNames = True
args.showFormulas = True
args.showCharges = True
# Read the compounds from the first file.
helper = BiochemHelper()
firstCompounds = helper.buildDictFromListOfObjects(
helper.readCompoundsFile(args.cpdfile1))
if (args.flatFile == False):
print('First compound file: %s' % (args.cpdfile1))
print(' Number of compounds: %d' % (len(firstCompounds)))
# Read the compounds from the second file.
secondCompounds = helper.buildDictFromListOfObjects(
helper.readCompoundsFile(args.cpdfile2))
if (args.flatFile == False):
print('Second compound file: %s' % (args.cpdfile2))
print(' Number of compounds: %d' % (len(secondCompounds)))
# Keep track of differences in compounds.
compoundsOnlyInFirst = list()
compoundsOnlyInSecond = list()
diffNames = set()
parser.add_argument('--show-charges', help='show details on compounds with different charges', action='store_true', dest='showCharges', default=False)
parser.add_argument('--flat', help='Prints out requested differences in a flat-file format', action='store_true', dest='flatFile', default=False)
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# The --show-details option turns on all of the detail options.
if args.showDetails:
args.showNames = True
args.showFormulas = True
args.showCharges = True
# Read the compounds from the first file.
helper = BiochemHelper()
firstCompounds = helper.buildDictFromListOfObjects(helper.readCompoundsFile(args.cpdfile1))
if(args.flatFile == False):
print 'First compound file: %s' %(args.cpdfile1)
print ' Number of compounds: %d' %(len(firstCompounds))
# Read the compounds from the second file.
secondCompounds = helper.buildDictFromListOfObjects(helper.readCompoundsFile(args.cpdfile2))
if(args.flatFile == False):
print 'Second compound file: %s' %(args.cpdfile2)
print ' Number of compounds: %d' %(len(secondCompounds))
# Keep track of differences in compounds.
compoundsOnlyInFirst = list()
compoundsOnlyInSecond = list()
diffNames = set()
diffFormulas = set()
