args.showBadAbbrs = True
args.showFormulas = True
args.showCharges = True
args.showCofactors = True
# Read the compounds from the specified file.
print 'Compound file: %s' % (args.cpdfile)
helper = BiochemHelper()
compounds = helper.readCompoundsFile(args.cpdfile)
if compounds is None:
print 'Error reading compounds file'
exit(1)
print 'Number of compounds: %d' % (len(compounds))
# Create a dictionary keyed by id for fast lookup of compounds.
compoundDict = helper.buildIndexDictFromListOfObjects(compounds)
# Check for duplicates, missing and invalid values.
idDict = dict()
duplicateId = 0
badIdChars = list()
nameDict = dict()
duplicateName = 0
badNameChars = list()
abbrDict = dict()
duplicateAbbr = 0
badAbbrChars = list()
noFormula = list()
largeCharge = list()
noCharge = list()
badCore = list()
args.showBadAbbrs = True
args.showFormulas = True
args.showCharges = True
args.showCofactors = True
# Read the compounds from the specified file.
print "Compound file: %s" % (args.cpdfile)
helper = BiochemHelper()
compounds = helper.readCompoundsFile(args.cpdfile)
if compounds is None:
print "Error reading compounds file"
exit(1)
print "Number of compounds: %d" % (len(compounds))
# Create a dictionary keyed by id for fast lookup of compounds.
compoundDict = helper.buildIndexDictFromListOfObjects(compounds)
# Check for duplicates, missing and invalid values.
idDict = dict()
duplicateId = 0
badIdChars = list()
nameDict = dict()
duplicateName = 0
badNameChars = list()
abbrDict = dict()
duplicateAbbr = 0
badAbbrChars = list()
noFormula = list()
largeCharge = list()
noCharge = list()
badCore = list()
args.showBadIds = True
args.showDupNames = True
args.showBadNames = True
args.showStatus = True
# Read the reactions from the specified file.
print 'Reaction file: %s' % (args.rxnfile)
helper = BiochemHelper()
reactions = helper.readReactionsFile(args.rxnfile)
if reactions is None:
print 'Error reading reactions file'
exit(1)
print 'Number of reactions: %d' % (len(reactions))
# Create a dictionary keyed by id for fast lookup of reactions.
reactionDict = helper.buildIndexDictFromListOfObjects(reactions)
# Check for duplicates, missing and invalid values.
idDict = dict()
duplicateId = 0
badIdChars = list()
nameDict = dict()
duplicateName = 0
badNameChars = list()
abbrDict = dict()
duplicateAbbr = 0
badAbbrChars = list()
badDirection = list()
badReversibility = list()
unknownReversibility = list()
diffEquationCode = list()
biochem['cues'] = list()
# The following fields are optional in a Biochemistry typed object.
if args.name is not None:
biochem['name'] = args.name
if args.description is not None:
biochem['description'] = args.description
# Create a helper object.
helper = BiochemHelper()
# Add the compounds from the compounds file.
print(('Adding compounds from %s ...' % (args.compoundfile)))
biochem['compounds'] = helper.readCompoundsFile(args.compoundfile,
includeLinenum=False)
compounds = helper.buildIndexDictFromListOfObjects(biochem['compounds'])
# Start with an empty dictionary of compartments. With compartment-free reactions, just add
# place holder compartments as they are found processing the reactions.
compartments = dict()
# Add the reactions from the reactions file.
print(('Adding reactions from %s ...' % (args.reactionfile)))
biochem['reactions'] = list()
reactions = helper.readReactionsFile(args.reactionfile,
includeLinenum=False)
for index in range(len(reactions)):
rxn = reactions[index]
reactants, products = helper.parseEquation(rxn['equation'])
if reactants is None and products is None: # @todo Need to confirm this
args.showBadIds = True
args.showDupNames = True
args.showBadNames = True
args.showStatus = True
# Read the reactions from the specified file.
print 'Reaction file: %s' %(args.rxnfile)
helper = BiochemHelper()
reactions = helper.readReactionsFile(args.rxnfile)
if reactions is None:
print 'Error reading reactions file'
exit(1)
print 'Number of reactions: %d' %(len(reactions))
# Create a dictionary keyed by id for fast lookup of reactions.
reactionDict = helper.buildIndexDictFromListOfObjects(reactions)
# Check for duplicates, missing and invalid values.
idDict = dict()
duplicateId = 0
badIdChars = list()
nameDict = dict()
duplicateName = 0
badNameChars = list()
abbrDict = dict()
duplicateAbbr = 0
badAbbrChars = list()
badDirection = list()
badReversibility = list()
unknownReversibility = list()
diffEquationCode = list()
biochem['compoundSets'] = list()
biochem['cues'] = list()
# The following fields are optional in a Biochemistry typed object.
if args.name is not None:
biochem['name'] = args.name
if args.description is not None:
biochem['description'] = args.description
# Create a helper object.
helper = BiochemHelper()
# Add the compounds from the compounds file.
print 'Adding compounds from %s ...' %(args.compoundfile)
biochem['compounds'] = helper.readCompoundsFile(args.compoundfile, includeLinenum=False)
compounds = helper.buildIndexDictFromListOfObjects(biochem['compounds'])
# Start with an empty dictionary of compartments. With compartment-free reactions, just add
# place holder compartments as they are found processing the reactions.
compartments = dict()
# Add the reactions from the reactions file.
print 'Adding reactions from %s ...' %(args.reactionfile)
biochem['reactions'] = list()
reactions = helper.readReactionsFile(args.reactionfile, includeLinenum=False)
for index in range(len(reactions)):
rxn = reactions[index]
reactants, products = helper.parseEquation(rxn['equation'])
if reactants is None and products is None: # @todo Need to confirm this
continue
