def __init__(self, compoundsPath, reactionsPath):
''' Initialize object.
@param compoundsPath: Path to master compounds file
@param reactionsPath: Path to master reactions file
@return Nothing
'''
# Load the master compounds and reactions from source files.
self.biochem = BiochemHelper()
self.masterCompoundsList = self.biochem.readCompoundsFile(compoundsPath, includeLinenum=False)
self.masterCompounds = self.buildIndexDictFromListOfObjects(self.masterCompoundsList)
self.masterReactionsList = self.biochem.readReactionsFile(reactionsPath, includeLinenum=False)
self.masterReactions = self.buildIndexDictFromListOfObjects(self.masterReactionsList)
# Create empty dictionaries for keeping track of items to add to Model Template.
self.compartments = dict()
self.biomasses = dict()
self.compounds = dict()
self.compCompounds = dict()
self.roles = dict()
self.complexes = dict()
self.reactions = dict()
return
def __init__(self, compoundsPath, reactionsPath):
''' Initialize object.
@param compoundsPath: Path to master compounds file
@param reactionsPath: Path to master reactions file
@return Nothing
'''
# Load the master compounds and reactions from source files.
self.biochem = BiochemHelper()
self.masterCompoundsList = self.biochem.readCompoundsFile(compoundsPath, includeLinenum=False)
self.masterCompounds = self.buildIndexDictFromListOfObjects(self.masterCompoundsList)
self.masterReactionsList = self.biochem.readReactionsFile(reactionsPath, includeLinenum=False)
self.masterReactions = self.buildIndexDictFromListOfObjects(self.masterReactionsList)
# Create empty dictionaries for keeping track of items to add to Model Template.
self.compartments = dict()
self.biomasses = dict()
self.compounds = dict()
self.compCompounds = dict()
self.roles = dict()
self.complexes = dict()
self.reactions = dict()
return
parser.add_argument('--show-bad-names', help='show details on bad names', action='store_true', dest='showBadNames', 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.showDupIds = True
args.showBadIds = True
args.showDupNames = True
args.showBadNames = True
# Read the complex role mapping from the specified file.
print('Complex role mapping file: %s' % args.cpxrolefile)
helper = BiochemHelper()
complexRoles = helper.readComplexRolesFile(args.cpxrolefile)
if complexRoles is None:
print('Error reading complex role mapping file')
exit(1)
print('Number of mappings: %d' % len(complexRoles))
# Check for duplicates, missing and invalid values.
complexIdDict = dict()
duplicateComplexId = 0
badComplexIdChars = list()
roleIdDict = dict()
duplicateRoleId = 0
badRoleIdChars = list()
complexNameDict = dict()
duplicateComplexName = 0
# The --show-details option turns on all of the detail options.
if args.showDetails:
args.showDupIds = True
args.showBadIds = True
args.showDupNames = True
args.showBadNames = True
args.showDupAbbrs = True
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
class TemplateHelper(BaseHelper):
def __init__(self, compoundsPath, reactionsPath):
''' Initialize object.
@param compoundsPath: Path to master compounds file
@param reactionsPath: Path to master reactions file
@return Nothing
'''
# Load the master compounds and reactions from source files.
self.biochem = BiochemHelper()
self.masterCompoundsList = self.biochem.readCompoundsFile(compoundsPath, includeLinenum=False)
self.masterCompounds = self.buildIndexDictFromListOfObjects(self.masterCompoundsList)
self.masterReactionsList = self.biochem.readReactionsFile(reactionsPath, includeLinenum=False)
self.masterReactions = self.buildIndexDictFromListOfObjects(self.masterReactionsList)
# Create empty dictionaries for keeping track of items to add to Model Template.
self.compartments = dict()
self.biomasses = dict()
self.compounds = dict()
self.compCompounds = dict()
self.roles = dict()
self.complexes = dict()
self.reactions = dict()
return
def readBiomassesFile(self, biomassPath, compoundsPath, includeLinenum=True, noFormat=False):
''' Read the contents of a biomasses and biomass compounds files.
There is one compound per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateBiomass structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param biomassPath: Path to biomasses file
@param compoundsPath: Path to biomass compounds file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in compound dictionary are not formatted
@return Nothing
'''
# Read the biomass compounds from the specified file.
compounds = dict()
with open(compoundsPath, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
required = { 'biomass_id', 'id', 'coefficient', 'coefficient_type', 'class',
'linked_compounds', 'compartment' }
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Biomass compound on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateBiomassComponent.
component = dict()
if noFormat:
for index in range(len(nameList)):
component[nameList[index]] = fields[index]
else:
compCompound = self.addCompCompound(fields[fieldNames['id']], fields[fieldNames['compartment']])
component['class'] = fields[fieldNames['class']]
component['templatecompcompound_ref'] = '~/compcompounds/id/'+compCompound['id']
component['coefficient_type'] = fields[fieldNames['coefficient_type']]
component['coefficient'] = float(fields[fieldNames['coefficient']])
component['linked_compound_refs'] = list()
component['link_coefficients'] = list()
if fields[fieldNames['linked_compounds']] != 'null':
linkedCpds = fields[fieldNames['linked_compounds']].split('|')
if len(linkedCpds) < 1:
raise LinkedCompoundFormatError('Biomass compound %s on line %d has an invalid linked compound field' %(fields[fieldNames['id']], linenum))
for lcIndex in range(len(linkedCpds)):
parts = linkedCpds[lcIndex].split(':')
if len(parts) != 2:
raise LinkedCompoundFormatError('Biomass compound %s on line %d has an invalid linked compound field' %(fields[fieldNames['id']], linenum))
linkCompCompound = self.addCompCompound(parts[0], fields[fieldNames['compartment']])
component['linked_compound_refs'].append('~/compcompounds/id/'+linkCompCompound['id'])
component['link_coefficients'].append(float(parts[1]))
if includeLinenum:
component['linenum'] = linenum
if fields[fieldNames['biomass_id']] not in compounds:
compounds[fields[fieldNames['biomass_id']]] = list()
compounds[fields[fieldNames['biomass_id']]].append(component)
# Read the biomasses from the specified file.
with open(biomassPath, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
required = { 'id', 'name', 'type', 'other', 'dna', 'rna', 'protein', 'lipid',
'cellwall', 'cofactor', 'energy' }
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Biomass on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateBiomass.
biomass = dict()
if noFormat:
for index in range(len(nameList)):
biomass[nameList[index]] = fields[index]
else:
biomass['id'] = fields[fieldNames['id']]
biomass['name'] = fields[fieldNames['name']]
biomass['type'] = fields[fieldNames['type']]
biomass['other'] = float(fields[fieldNames['other']])
biomass['dna'] = float(fields[fieldNames['dna']])
biomass['rna'] = float(fields[fieldNames['rna']])
biomass['protein'] = float(fields[fieldNames['protein']])
biomass['lipid'] = float(fields[fieldNames['lipid']])
biomass['cellwall'] = float(fields[fieldNames['cellwall']])
biomass['cofactor'] = float(fields[fieldNames['cofactor']])
biomass['energy'] = float(fields[fieldNames['energy']])
biomass['templateBiomassComponents'] = compounds[biomass['id']]
if includeLinenum:
biomass['linenum'] = linenum
if biomass['id'] not in self.biomasses:
self.biomasses[biomass['id']] = biomass
else:
raise DuplicateBiomassError('Biomass %s on line %d is a duplicate' %(biomass['id'], linenum))
return
def readCompartmentsFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a compartments file.
There is one compartment per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateCompartment structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param path: Path to compartments file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in compound dictionary are not formatted
@return Nothing
'''
# The following fields are required in a compartments file.
required = { 'index', 'id', 'name', 'hierarchy', 'pH', 'aliases' }
# Read the compartments from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Compartment on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateCompartment.
compartment = dict()
if noFormat:
for index in range(len(nameList)):
compartment[nameList[index]] = fields[index]
else:
compartment['index'] = fields[fieldNames['index']]
compartment['id'] = fields[fieldNames['id']]
compartment['name'] = fields[fieldNames['name']]
compartment['hierarchy'] = int(fields[fieldNames['hierarchy']])
compartment['pH'] = float(fields[fieldNames['pH']])
compartment['aliases'] = list()
if fields[fieldNames['aliases']] != 'null':
self.addToList(fields[fieldNames['aliases']], ';', compartment['aliases'])
if includeLinenum:
compartment['linenum'] = linenum
if compartment['id'] not in self.compartments:
self.compartments[compartment['id']] = compartment
else:
raise DuplicateCompartmentError('Compartment %s on line %d is a duplicate' %(compartment['id'], linenum))
return
def readRolesFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a roles file.
There is one role per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateRole structure uses the field names as keys. When noFormat
is True, the field values are exactly as read from the file. Otherwise,
the fields with a null value are converted to default values and numeric
values are converted to numbers.
@param path: Path to roles file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in TemplateRole dictionary are not formatted
@return Nothing
'''
# The following fields are required in a reactions file.
required = { 'id', 'name', 'source', 'features', 'aliases' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Role on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateCompartment.
role = dict()
if noFormat:
for index in range(len(nameList)):
role[nameList[index]] = fields[index]
else:
role['id'] = fields[fieldNames['id']]
role['name'] = fields[fieldNames['name']]
role['source'] = fields[fieldNames['source']]
role['features'] = list()
if fields[fieldNames['features']] != 'null':
self.addToList(fields[fieldNames['features']], ';', role['features'])
role['aliases'] = list()
if fields[fieldNames['aliases']] != 'null':
self.addToList(fields[fieldNames['aliases']], ';', role['aliases'])
# role['aliases'] = self.makeAliases(fields[fieldNames['aliases']], '///', ':')
if includeLinenum:
role['linenum'] = linenum
if role['id'] not in self.roles:
self.roles[role['id']] = role
else:
raise DuplicateRoleError('Role %s on line %d is a duplicate' %(role['id'], linenum))
return
def readComplexesFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a complex roles file.
There is one complex per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateComplex structure uses the field names as keys. When noFormat
is True, the field values are exactly as read from the file. Otherwise, the
fields with a null value are converted to default values and numeric values
are converted to numbers.
@param path: Path to complex roles file
@param includeLinenum: When True, include line number in dictionary
@return Nothing
'''
# The following fields are required in a complexes file.
required = { 'id', 'name', 'source', 'reference', 'confidence', 'roles' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Role on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateComplex if needed. The same complex can be paired with multiple roles.
complex = dict()
if noFormat:
for index in range(len(nameList)):
role[nameList[index]] = fields[index]
else:
complex['id'] = fields[fieldNames['id']]
complex['name'] = fields[fieldNames['name']]
complex['source'] = fields[fieldNames['source']]
complex['reference'] = fields[fieldNames['reference']]
complex['confidence'] = float(fields[fieldNames['confidence']])
complex['complexroles'] = list()
if fields[fieldNames['roles']] != 'null':
# Link the role and complex through a TemplateComplexRole.
links = fields[fieldNames['roles']].split('|')
for index in range(len(links)):
values = links[index].split(';')
if values[0] not in self.roles:
raise RoleNotFoundError('Role %s on line %d not found' %(values[0], linenum))
complexRole = dict()
complexRole['templaterole_ref'] = '~/roles/id/'+values[0] # Need to validate
complexRole['optional'] = int(values[2])
complexRole['triggering'] = int(values[3])
complex['complexroles'].append(complexRole)
if includeLinenum:
complex['linenum'] = linenum
if complex['id'] not in self.complexes:
self.complexes[complex['id']] = complex
else:
raise DuplicateComplexError('Complex %s on line %d is a duplicate' %(role['id'], linenum))
return
def readReactionsFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a reactions file.
There is one reaction per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateReaction structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param path: Path to reactions file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in reaction dictionary are not formatted
@return Nothing
'''
# Keep track of these statistics.
self.numConditional = 0
self.numGapfilling = 0
self.numSpontaneous = 0
self.numUniversal = 0
# The following fields are required in a reactions file.
required = { 'id', 'compartment', 'direction', 'gfdir', 'type', 'base_cost',
'forward_cost', 'reverse_cost', 'complexes' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Reaction on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateReaction.
reaction = dict()
if noFormat:
for index in range(len(nameList)):
reaction[nameList[index]] = fields[index]
else:
# Get the reaction from the master list.
reactionId = fields[fieldNames['id']]
try:
masterReaction = self.masterReactionsList[self.masterReactions[reactionId]]
except:
raise ReactionNotFoundError('Reaction %s not found in master biochemistry' %(reactionId))
# Check the reaction status.
#if 'OK' not in masterReaction['status']:
# print 'WARNING: Reaction %s has status %s and was skipped' %(masterReaction['id'], masterReaction['status'])
# continue
# Check for obsolete reaction.
if masterReaction['is_obsolete']:
if masterReaction['linked_reaction'] != 'null':
# One of the reactions in the list is not obsolete.
linkIds = masterReaction['linked_reaction'].split(';')
for index in range(len(linkIds)):
try:
linkReaction = self.masterReactionsList[self.masterReactions[linkIds[index]]]
if not linkReaction['is_obsolete']:
print 'NOTICE: Obsolete reaction %s replaced by %s' %(masterReaction['id'], linkReaction['id'])
masterReaction = linkReaction
break
except KeyError as e:
raise ObsoleteReactionError('Reaction %s is obsolete and replacement %s not found' %(masterReaction['id'], linkIds[index]))
if masterReaction['is_obsolete']:
raise ObsoleteReactionError('Reaction %s is obsolete and all replacements are obsolete' %(masterReaction['id']))
else:
raise ObsoleteReactionError('Reaction %s is obsolete and no replacement is specified' %(masterReaction['id']))
# Make sure all of the compartments are valid.
compartmentIds = fields[fieldNames['compartment']].split('|')
idcomp = compartmentIds[0]
for cindex in range(len(compartmentIds)):
try:
self.compartments[compartmentIds[cindex]]
except KeyError as e:
raise CompartmentNotFoundError('Compartment %s not found in current list' %(compartmentIds[cindex]))
# Build the TemplateReaction.
reaction['id'] = '%s_%s' %(reactionId, idcomp) # Use first compartment for suffix
reaction['name'] = masterReaction['name']
reaction['deltaG'] = masterReaction['deltag']
reaction['deltaGErr'] = masterReaction['deltagerr']
reaction['status'] = masterReaction['status']
reaction['reversibility'] = masterReaction['reversibility']
reaction['direction'] = fields[fieldNames['direction']]
if fields[fieldNames['gfdir']] == 'null':
reaction['GapfillDirection'] = ''
else:
reaction['GapfillDirection'] = fields[fieldNames['gfdir']]
reaction['type'] = fields[fieldNames['type']]
reaction['maxforflux'] = float(100)
reaction['maxrevflux'] = float(-100)
reaction['templatecompartment_ref'] = '~/compartments/id/'+compartmentIds[0]
reaction['base_cost'] = float(fields[fieldNames['base_cost']])
reaction['forward_penalty'] = float(fields[fieldNames['forward_cost']])
reaction['reverse_penalty'] = float(fields[fieldNames['reverse_cost']])
reaction['templateReactionReagents'] = list()
# Stoichiometry format is n:cpdid:c:i:"cpdname"
if len(masterReaction['stoichiometry']) > 0:
try:
reagents = masterReaction['stoichiometry'].split(';')
for rindex in range(len(reagents)):
parts = reagents[rindex].split(':')
compartmentIndex = int(parts[2])
compCompound = self.addCompCompound(parts[1], compartmentIds[compartmentIndex])
templateReactionReagent = dict()
templateReactionReagent['templatecompcompound_ref'] = '~/compcompounds/id/'+compCompound['id']
templateReactionReagent['coefficient'] = float(parts[0])
reaction['templateReactionReagents'].append(templateReactionReagent)
except IndexError as e:
raise ReactionFormatError('Reaction %s on line %d has invalid stoichiometry "%s" in master reaction' %(reaction['id'], linenum, masterReaction['stoichiometry']))
reaction['templatecomplex_refs'] = list()
if reaction['type'] == 'conditional' and fields[fieldNames['complexes']] == 'null':
raise NoComplexesError('Reaction %s is of type conditional and no complexes are specified' %(reactionId))
if fields[fieldNames['complexes']] != 'null':
complexes = fields[fieldNames['complexes']].split('|')
for cindex in range(len(complexes)):
if complexes[cindex] in self.complexes:
reaction['templatecomplex_refs'].append('~/complexes/id/'+complexes[cindex])
else:
print 'Reaction %s on line %d refers to complex %s which is not found' %(reaction['id'], linenum, complexes[cindex])
# raise ComplexNotFoundError('Reaction %s on line %d refers to complex %s which is not found' %(reaction['id'], linenum, complexes[cindex]))
if reaction['type'] == 'gapfilling':
print 'NOTICE: Reaction %s on line %d has complexes but is not of type conditional' %(reaction['id'], linenum)
if includeLinenum:
reaction['linenum'] = linenum
# Check for duplicates.
if reaction['id'] not in self.reactions:
self.reactions[reaction['id']] = reaction
if reaction['type'] == 'conditional':
self.numConditional += 1
elif reaction['type'] == 'gapfilling':
self.numGapfilling += 1
elif reaction['type'] == 'spontaneous':
self.numSpontaneous += 1
elif reaction['type'] == 'universal':
self.numUniversal += 1
else:
raise DuplicateReactionError('Reaction %s on line %d is a duplicate' %(reaction['id'], linenum))
return
def addCompCompound(self, compoundId, compartmentId):
''' Add a compound to the model template.
@param compoundId: Compound ID in master compound list
@param compartmentId: Compartment ID
@return TemplateCompCompound structure
'''
# Get the compound from the master list.
try:
masterCompound = self.masterCompoundsList[self.masterCompounds[compoundId]]
except KeyError as e:
raise CompoundNotFoundError('Compound %s not found in master biochemistry' %(compoundId))
# Check for obsolete compound.
if masterCompound['is_obsolete']:
if masterCompound['linked_compound'] != 'null':
linkIds = masterCompound['linked_compound'].split(';')
# One of the compounds in the list is not obsolete.
for index in range(len(linkIds)):
try:
linkCompound = self.masterCompoundsList[self.masterCompounds[linkIds[index]]]
if not linkCompound['is_obsolete']:
print 'NOTICE: Obsolete compound %s replaced by %s' %(masterCompound['id'], linkCompound['id'])
masterCompound = linkCompound
break
except KeyError as e:
raise ObsoleteCompoundError('Compound %s is obsolete and replacement %s not found' %(masterCompound['id'], linkIds[index]))
if masterCompound['is_obsolete']:
raise ObsoleteCompoundError('Compound %s is obsolete and all replacements are obsolete' %(masterCompound['id']))
else:
raise ObsoleteCompoundError('Compound %s is obsolete and no replacement is specified' %(masterCompound['id']))
# If needed, create a new TemplateCompound and add it to the Model Template.
if compoundId not in self.compounds:
try:
compound = dict()
compound['id'] = masterCompound['id']
compound['name'] = masterCompound['name']
compound['abbreviation'] = masterCompound['abbreviation']
compound['isCofactor'] = masterCompound['is_cofactor']
compound['aliases'] = masterCompound['aliases']
compound['defaultCharge'] = masterCompound['charge']
compound['mass'] = masterCompound['mass']
if compound['mass'] == 'null':
compound['mass'] = 0
compound['deltaG'] = masterCompound['deltag']
compound['deltaGErr'] = masterCompound['deltagerr']
compound['formula'] = masterCompound['formula']
self.compounds[compound['id']] = compound
except KeyError as e:
raise CompoundKeyError('Missing key in compound %s: %s' %(masterCompound['id'], e.message))
else:
compound = self.compounds[compoundId]
# The id for TemplateCompCompound includes the compartment suffix.
try:
compartment = self.compartments[compartmentId]
except KeyError as e:
raise CompartmentNotFoundError('Compartment %s not found in current list' %(compartmentId))
id = '%s_%s' %(compoundId, compartmentId)
# If needed, create a new TemplateCompCompound and add it to the Model Template.
if id not in self.compCompounds:
compCompound = dict()
compCompound['id'] = id
compCompound['templatecompound_ref'] = '~/compounds/id/'+compoundId
compCompound['charge'] = compound['defaultCharge'] # @todo Not sure how charge could be different
if compartment['id'] == 'e':
compCompound['maxuptake'] = 100.0 # Set a maximum for the extracellular compartment
else:
compCompound['maxuptake'] = 0.0
compCompound['templatecompartment_ref'] = '~/compartments/id/'+compartmentId
self.compCompounds[id] = compCompound
else:
compCompound = self.compCompounds[id]
return compCompound
biochem['reactions'] = list()
biochem['reactionSets'] = list()
biochem['compoundSets'] = list()
biochem['cues'] = list()
biochem['compound_aliases'] = dict()
biochem['reaction_aliases'] = dict()
# The following fields are optional in a Biochemistry object.
if args.name is not None:
biochem['name'] = args.name
if args.description is not None:
biochem['description'] = args.description
# Add the compounds from the compounds file. Required fields: id, name,
# name, abbreviation, formula, defaultCharge, isCofactor
helper = BiochemHelper()
compounds = helper.readCompoundsFile(args.compoundfile,
includeLinenum=False)
for index in range(len(compounds)):
biochem['compounds'].append(compounds[index])
# Add the reactions from the reactions file. Required fields: id, name,
# abbreviation, direction, thermoReversibility, status, defaultProtons, reagents.
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
parser.add_argument('--show-names', help='show details on reactions with different names', action='store_true', dest='showNames', default=False)
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()
biochem = dict()
biochem['id'] = args.id
# The following fields are required in a Biochemistry typed object but they are currently unused.
biochem['reactionSets'] = 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)
class TemplateHelper(BaseHelper):
def __init__(self, compoundsPath, reactionsPath):
''' Initialize object.
@param compoundsPath: Path to master compounds file
@param reactionsPath: Path to master reactions file
@return Nothing
'''
# Load the master compounds and reactions from source files.
self.biochem = BiochemHelper()
self.masterCompoundsList = self.biochem.readCompoundsFile(compoundsPath, includeLinenum=False)
self.masterCompounds = self.buildIndexDictFromListOfObjects(self.masterCompoundsList)
self.masterReactionsList = self.biochem.readReactionsFile(reactionsPath, includeLinenum=False)
self.masterReactions = self.buildIndexDictFromListOfObjects(self.masterReactionsList)
# Create empty dictionaries for keeping track of items to add to Model Template.
self.compartments = dict()
self.biomasses = dict()
self.compounds = dict()
self.compCompounds = dict()
self.roles = dict()
self.complexes = dict()
self.reactions = dict()
return
def readBiomassesFile(self, biomassPath, compoundsPath, includeLinenum=True, noFormat=False):
''' Read the contents of a biomasses and biomass compounds files.
There is one compound per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateBiomass structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param biomassPath: Path to biomasses file
@param compoundsPath: Path to biomass compounds file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in compound dictionary are not formatted
@return Nothing
'''
# Read the biomass compounds from the specified file.
compounds = dict()
with open(compoundsPath, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
required = { 'biomass_id', 'id', 'coefficient', 'coefficient_type', 'class',
'linked_compounds', 'compartment' }
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Biomass compound on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateBiomassComponent.
component = dict()
if noFormat:
for index in range(len(nameList)):
component[nameList[index]] = fields[index]
else:
compCompound = self.addCompCompound(fields[fieldNames['id']], fields[fieldNames['compartment']])
component['class'] = fields[fieldNames['class']]
component['templatecompcompound_ref'] = '~/compcompounds/id/'+compCompound['id']
component['coefficient_type'] = fields[fieldNames['coefficient_type']]
component['coefficient'] = float(fields[fieldNames['coefficient']])
component['linked_compound_refs'] = list()
component['link_coefficients'] = list()
if fields[fieldNames['linked_compounds']] != 'null':
linkedCpds = fields[fieldNames['linked_compounds']].split('|')
if len(linkedCpds) < 1:
raise LinkedCompoundFormatError('Biomass compound %s on line %d has an invalid linked compound field' %(fields[fieldNames['id']], linenum))
for lcIndex in range(len(linkedCpds)):
parts = linkedCpds[lcIndex].split(':')
if len(parts) != 2:
raise LinkedCompoundFormatError('Biomass compound %s on line %d has an invalid linked compound field' %(fields[fieldNames['id']], linenum))
linkCompCompound = self.addCompCompound(parts[0], fields[fieldNames['compartment']])
component['linked_compound_refs'].append('~/compcompounds/id/'+linkCompCompound['id'])
component['link_coefficients'].append(float(parts[1]))
if includeLinenum:
component['linenum'] = linenum
if fields[fieldNames['biomass_id']] not in compounds:
compounds[fields[fieldNames['biomass_id']]] = list()
compounds[fields[fieldNames['biomass_id']]].append(component)
# Read the biomasses from the specified file.
with open(biomassPath, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
required = { 'id', 'name', 'type', 'other', 'dna', 'rna', 'protein', 'lipid',
'cellwall', 'cofactor', 'energy' }
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Biomass on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateBiomass.
biomass = dict()
if noFormat:
for index in range(len(nameList)):
biomass[nameList[index]] = fields[index]
else:
biomass['id'] = fields[fieldNames['id']]
biomass['name'] = fields[fieldNames['name']]
biomass['type'] = fields[fieldNames['type']]
biomass['other'] = float(fields[fieldNames['other']])
biomass['dna'] = float(fields[fieldNames['dna']])
biomass['rna'] = float(fields[fieldNames['rna']])
biomass['protein'] = float(fields[fieldNames['protein']])
biomass['lipid'] = float(fields[fieldNames['lipid']])
biomass['cellwall'] = float(fields[fieldNames['cellwall']])
biomass['cofactor'] = float(fields[fieldNames['cofactor']])
biomass['energy'] = float(fields[fieldNames['energy']])
biomass['templateBiomassComponents'] = compounds[biomass['id']]
if includeLinenum:
biomass['linenum'] = linenum
if biomass['id'] not in self.biomasses:
self.biomasses[biomass['id']] = biomass
else:
raise DuplicateBiomassError('Biomass %s on line %d is a duplicate' %(biomass['id'], linenum))
return
def readCompartmentsFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a compartments file.
There is one compartment per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateCompartment structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param path: Path to compartments file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in compound dictionary are not formatted
@return Nothing
'''
# The following fields are required in a compartments file.
required = { 'index', 'id', 'name', 'hierarchy', 'pH', 'aliases' }
# Read the compartments from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Compartment on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateCompartment.
compartment = dict()
if noFormat:
for index in range(len(nameList)):
compartment[nameList[index]] = fields[index]
else:
compartment['index'] = fields[fieldNames['index']]
compartment['id'] = fields[fieldNames['id']]
compartment['name'] = fields[fieldNames['name']]
compartment['hierarchy'] = int(fields[fieldNames['hierarchy']])
compartment['pH'] = float(fields[fieldNames['pH']])
compartment['aliases'] = list()
if fields[fieldNames['aliases']] != 'null':
self.addToList(fields[fieldNames['aliases']], ';', compartment['aliases'])
if includeLinenum:
compartment['linenum'] = linenum
if compartment['id'] not in self.compartments:
self.compartments[compartment['id']] = compartment
else:
raise DuplicateCompartmentError('Compartment %s on line %d is a duplicate' %(compartment['id'], linenum))
return
def readRolesFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a roles file.
There is one role per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateRole structure uses the field names as keys. When noFormat
is True, the field values are exactly as read from the file. Otherwise,
the fields with a null value are converted to default values and numeric
values are converted to numbers.
@param path: Path to roles file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in TemplateRole dictionary are not formatted
@return Nothing
'''
# The following fields are required in a reactions file.
required = { 'id', 'name', 'source', 'features', 'aliases' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Role on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateCompartment.
role = dict()
if noFormat:
for index in range(len(nameList)):
role[nameList[index]] = fields[index]
else:
role['id'] = fields[fieldNames['id']]
role['name'] = fields[fieldNames['name']]
role['source'] = fields[fieldNames['source']]
role['features'] = list()
if fields[fieldNames['features']] != 'null':
self.addToList(fields[fieldNames['features']], ';', role['features'])
role['aliases'] = list()
if fields[fieldNames['aliases']] != 'null':
self.addToList(fields[fieldNames['aliases']], ';', role['aliases'])
# role['aliases'] = self.makeAliases(fields[fieldNames['aliases']], '///', ':')
if includeLinenum:
role['linenum'] = linenum
if role['id'] not in self.roles:
self.roles[role['id']] = role
else:
raise DuplicateRoleError('Role %s on line %d is a duplicate' %(role['id'], linenum))
return
def readComplexesFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a complex roles file.
There is one complex per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateComplex structure uses the field names as keys. When noFormat
is True, the field values are exactly as read from the file. Otherwise, the
fields with a null value are converted to default values and numeric values
are converted to numbers.
@param path: Path to complex roles file
@param includeLinenum: When True, include line number in dictionary
@return Nothing
'''
# The following fields are required in a complexes file.
required = { 'id', 'name', 'source', 'reference', 'confidence', 'roles' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Role on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateComplex if needed. The same complex can be paired with multiple roles.
complex = dict()
if noFormat:
for index in range(len(nameList)):
role[nameList[index]] = fields[index]
else:
complex['id'] = fields[fieldNames['id']]
complex['name'] = fields[fieldNames['name']]
complex['source'] = fields[fieldNames['source']]
complex['reference'] = fields[fieldNames['reference']]
complex['confidence'] = float(fields[fieldNames['confidence']])
complex['complexroles'] = list()
if fields[fieldNames['roles']] != 'null':
# Link the role and complex through a TemplateComplexRole.
links = fields[fieldNames['roles']].split('|')
for index in range(len(links)):
values = links[index].split(';')
if values[0] not in self.roles:
raise RoleNotFoundError('Role %s on line %d not found' %(values[0], linenum))
complexRole = dict()
complexRole['templaterole_ref'] = '~/roles/id/'+values[0] # Need to validate
complexRole['optional'] = int(values[2])
complexRole['triggering'] = int(values[3])
complex['complexroles'].append(complexRole)
if includeLinenum:
complex['linenum'] = linenum
if complex['id'] not in self.complexes:
self.complexes[complex['id']] = complex
else:
raise DuplicateComplexError('Complex %s on line %d is a duplicate' %(role['id'], linenum))
return
def readReactionsFile(self, path, includeLinenum=True, noFormat=False):
''' Read the contents of a reactions file.
There is one reaction per line in the file with fields separated by tabs.
The first line of the file is a header with the field names.
The TemplateReaction structure uses the field names as keys. When
noFormat is True, the field values are exactly as read from the file.
Otherwise, the fields with a null value are converted to default values
and numeric values are converted to numbers.
@param path: Path to reactions file
@param includeLinenum: When True, include line number in dictionary
@param noFormat: When True, values in reaction dictionary are not formatted
@return Nothing
'''
# The following fields are required in a reactions file.
required = { 'id', 'compartment', 'direction', 'gfdir', 'type', 'base_cost',
'forward_cost', 'reverse_cost', 'complexes' }
# Read the reactions from the specified file.
with open(path, 'r') as handle:
# The first line has the header with the field names.
nameList = handle.readline().strip().split('\t')
fieldNames = self.validateHeader(nameList, required)
linenum = 1
for line in handle:
linenum += 1
fields = line.strip().split('\t')
if len(fields) < len(required):
print 'WARNING: Reaction on line %d is missing one or more fields, %s' %(linenum, fields)
continue
# Create a new TemplateReaction.
reaction = dict()
if noFormat:
for index in range(len(nameList)):
reaction[nameList[index]] = fields[index]
else:
# Get the reaction from the master list.
reactionId = fields[fieldNames['id']]
try:
masterReaction = self.masterReactionsList[self.masterReactions[reactionId]]
except:
raise ReactionNotFoundError('Reaction %s not found in master biochemistry' %(reactionId))
# Check the reaction status.
#if 'OK' not in masterReaction['status']:
# print 'WARNING: Reaction %s has status %s and was skipped' %(masterReaction['id'], masterReaction['status'])
# continue
# Check for obsolete reaction.
if masterReaction['is_obsolete']:
if masterReaction['linked_reaction'] != 'null':
# One of the reactions in the list is not obsolete.
linkIds = masterReaction['linked_reaction'].split(';')
for index in range(len(linkIds)):
try:
linkReaction = self.masterReactionsList[self.masterReactions[linkIds[index]]]
if not linkReaction['is_obsolete']:
print 'NOTICE: Obsolete reaction %s replaced by %s' %(masterReaction['id'], linkReaction['id'])
masterReaction = linkReaction
break
except KeyError as e:
raise ObsoleteReactionError('Reaction %s is obsolete and replacement %s not found' %(masterReaction['id'], linkIds[index]))
if masterReaction['is_obsolete']:
raise ObsoleteReactionError('Reaction %s is obsolete and all replacements are obsolete' %(masterReaction['id']))
else:
raise ObsoleteReactionError('Reaction %s is obsolete and no replacement is specified' %(masterReaction['id']))
# Make sure all of the compartments are valid.
compartmentIds = fields[fieldNames['compartment']].split('|')
idcomp = compartmentIds[0]
for cindex in range(len(compartmentIds)):
try:
self.compartments[compartmentIds[cindex]]
except KeyError as e:
raise CompartmentNotFoundError('Compartment %s not found in current list' %(compartmentIds[cindex]))
# Build the TemplateReaction.
reaction['id'] = '%s_%s' %(reactionId, idcomp) # Use first compartment for suffix
reaction['name'] = masterReaction['name']
reaction['deltaG'] = masterReaction['deltag']
reaction['deltaGErr'] = masterReaction['deltagerr']
reaction['status'] = masterReaction['status']
reaction['reversibility'] = masterReaction['reversibility']
reaction['direction'] = fields[fieldNames['direction']]
if fields[fieldNames['gfdir']] == 'null':
reaction['GapfillDirection'] = ''
else:
reaction['GapfillDirection'] = fields[fieldNames['gfdir']]
reaction['type'] = fields[fieldNames['type']]
reaction['maxforflux'] = float(100)
reaction['maxrevflux'] = float(-100)
reaction['templatecompartment_ref'] = '~/compartments/id/'+compartmentIds[0]
reaction['base_cost'] = float(fields[fieldNames['base_cost']])
reaction['forward_penalty'] = float(fields[fieldNames['forward_cost']])
reaction['reverse_penalty'] = float(fields[fieldNames['reverse_cost']])
reaction['templateReactionReagents'] = list()
# Stoichiometry format is n:cpdid:c:i:"cpdname"
if len(masterReaction['stoichiometry']) > 0:
try:
reagents = masterReaction['stoichiometry'].split(';')
for rindex in range(len(reagents)):
parts = reagents[rindex].split(':')
compartmentIndex = int(parts[2])
compCompound = self.addCompCompound(parts[1], compartmentIds[compartmentIndex])
templateReactionReagent = dict()
templateReactionReagent['templatecompcompound_ref'] = '~/compcompounds/id/'+compCompound['id']
templateReactionReagent['coefficient'] = float(parts[0])
reaction['templateReactionReagents'].append(templateReactionReagent)
except IndexError as e:
raise ReactionFormatError('Reaction %s on line %d has invalid stoichiometry "%s" in master reaction' %(reaction['id'], linenum, masterReaction['stoichiometry']))
reaction['templatecomplex_refs'] = list()
if reaction['type'] == 'conditional' and fields[fieldNames['complexes']] == 'null':
raise NoComplexesError('Reaction %s is of type conditional and no complexes are specified' %(reactionId))
if fields[fieldNames['complexes']] != 'null':
complexes = fields[fieldNames['complexes']].split('|')
for cindex in range(len(complexes)):
if complexes[cindex] in self.complexes:
reaction['templatecomplex_refs'].append('~/complexes/id/'+complexes[cindex])
else:
# print 'Reaction %s on line %d refers to complex %s which is not found' %(reaction['id'], linenum, complexes[cindex])
raise ComplexNotFoundError('Reaction %s on line %d refers to complex %s which is not found' %(reaction['id'], linenum, complexes[cindex]))
if includeLinenum:
reaction['linenum'] = linenum
# Check for duplicates.
if reaction['id'] not in self.reactions:
self.reactions[reaction['id']] = reaction
else:
raise DuplicateReactionError('Reaction %s on line %d is a duplicate' %(reaction['id'], linenum))
return
def addCompCompound(self, compoundId, compartmentId):
''' Add a compound to the model template.
@param compoundId: Compound ID in master compound list
@param compartmentId: Compartment ID
@return TemplateCompCompound structure
'''
# Get the compound from the master list.
try:
masterCompound = self.masterCompoundsList[self.masterCompounds[compoundId]]
except KeyError as e:
raise CompoundNotFoundError('Compound %s not found in master biochemistry' %(compoundId))
# Check for obsolete compound.
if masterCompound['is_obsolete']:
if masterCompound['linked_compound'] != 'null':
linkIds = masterCompound['linked_compound'].split(';')
# One of the compounds in the list is not obsolete.
for index in range(len(linkIds)):
try:
linkCompound = self.masterCompoundsList[self.masterCompounds[linkIds[index]]]
if not linkCompound['is_obsolete']:
print 'NOTICE: Obsolete compound %s replaced by %s' %(masterCompound['id'], linkCompound['id'])
masterCompound = linkCompound
break
except KeyError as e:
raise ObsoleteCompoundError('Compound %s is obsolete and replacement %s not found' %(masterCompound['id'], linkIds[index]))
if masterCompound['is_obsolete']:
raise ObsoleteCompoundError('Compound %s is obsolete and all replacements are obsolete' %(masterCompound['id']))
else:
raise ObsoleteCompoundError('Compound %s is obsolete and no replacement is specified' %(masterCompound['id']))
# If needed, create a new TemplateCompound and add it to the Model Template.
if compoundId not in self.compounds:
try:
compound = dict()
compound['id'] = masterCompound['id']
compound['name'] = masterCompound['name']
compound['abbreviation'] = masterCompound['abbreviation']
compound['isCofactor'] = masterCompound['is_cofactor']
compound['aliases'] = masterCompound['aliases']
compound['defaultCharge'] = masterCompound['charge']
compound['mass'] = masterCompound['mass']
if compound['mass'] == 'null':
compound['mass'] = 0
compound['deltaG'] = masterCompound['deltag']
compound['deltaGErr'] = masterCompound['deltagerr']
compound['formula'] = masterCompound['formula']
self.compounds[compound['id']] = compound
except KeyError as e:
raise CompoundKeyError('Missing key in compound %s: %s' %(masterCompound['id'], e.message))
else:
compound = self.compounds[compoundId]
# The id for TemplateCompCompound includes the compartment suffix.
try:
compartment = self.compartments[compartmentId]
except KeyError as e:
raise CompartmentNotFoundError('Compartment %s not found in current list' %(compartmentId))
id = '%s_%s' %(compoundId, compartmentId)
# If needed, create a new TemplateCompCompound and add it to the Model Template.
if id not in self.compCompounds:
compCompound = dict()
compCompound['id'] = id
compCompound['templatecompound_ref'] = '~/compounds/id/'+compoundId
compCompound['charge'] = compound['defaultCharge'] # @todo Not sure how charge could be different
if compartment['id'] == 'e':
compCompound['maxuptake'] = 100.0 # Set a maximum for the extracellular compartment
else:
compCompound['maxuptake'] = 0.0
compCompound['templatecompartment_ref'] = '~/compartments/id/'+compartmentId
self.compCompounds[id] = compCompound
else:
compCompound = self.compCompounds[id]
return compCompound
# The --show-details option turns on all of the detail options.
if args.showDetails:
args.showDupIds = True
args.showBadIds = True
args.showDupNames = True
args.showBadNames = True
args.showDupAbbrs = True
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
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.showDupIds = True
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
biochem = dict()
biochem['id'] = args.id
# The following fields are required in a Biochemistry typed object but they are currently unused.
biochem['reactionSets'] = 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,
'''
if __name__ == '__main__':
# Parse options.
parser = argparse.ArgumentParser(formatter_class=argparse.RawDescriptionHelpFormatter, prog='Build_SOLR_Tables', epilog=desc3)
parser.add_argument('--outputdir', help='path to output directory for storing SOLR tables', action='store', default='../SOLRDump')
parser.add_argument('--compoundfile', help='path to source master compounds file', action='store', default='../Biochemistry/compounds.master.tsv')
parser.add_argument('--reactionfile', help='path to source master reactions file', action='store', default='../Biochemistry/reactions.master.tsv')
parser.add_argument('--aliasdir', help='path to directory with source aliases files', action='store', default='../Aliases')
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create a helper for working with source files.
helper = BiochemHelper()
# Get the aliases from all of the aliases files.
compoundAliases, reactionAliases = helper.readAliasFiles(args.aliasdir)
# Get the compounds from the master compounds file.
compounds = helper.readCompoundsFile(args.compoundfile, includeLinenum=False, noFormat=True)
# Build the compounds file.
compoundHeader = [ 'id', 'abbreviation', 'name', 'formula', 'mass', 'source',
'structure', 'charge', 'is_core', 'is_obsolete', 'linked_compound',
'is_cofactor', 'deltag', 'deltagerr', 'pka', 'pkb',
'abstract_compound', 'comprised_of', 'aliases' ]
compoundFile = os.path.join(args.outputdir, 'Compounds.tsv')
with open(compoundFile, 'w') as handle:
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.showDupIds = True
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
parser.add_argument('--show-formulas', help='show details on compounds with different formulas', action='store_true', dest='showFormulas', default=False)
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()
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()
default='../Biochemistry/compounds.master.tsv')
parser.add_argument('--reactionfile',
help='path to source master reactions file',
action='store',
default='../Biochemistry/reactions.master.tsv')
parser.add_argument('--aliasdir',
help='path to directory with source aliases files',
action='store',
default='../Aliases')
usage = parser.format_usage()
parser.description = desc1 + ' ' + usage + desc2
parser.usage = argparse.SUPPRESS
args = parser.parse_args()
# Create a helper for working with source files.
helper = BiochemHelper()
# Get the aliases from all of the aliases files.
compoundAliases, reactionAliases = helper.readAliasFiles(args.aliasdir)
# Get the compounds from the master compounds file.
compounds = helper.readCompoundsFile(args.compoundfile,
includeLinenum=False,
noFormat=True)
# Build the compounds file.
compoundHeader = [
'id', 'abbreviation', 'name', 'formula', 'mass', 'source', 'structure',
'charge', 'is_core', 'is_obsolete', 'linked_compound', 'is_cofactor',
'deltag', 'deltagerr', 'pka', 'pkb', 'abstract_compound',
'comprised_of', 'aliases'
biochem['reactions'] = list()
biochem['reactionSets'] = list()
biochem['compoundSets'] = list()
biochem['cues'] = list()
biochem['compound_aliases'] = dict()
biochem['reaction_aliases'] = dict()
# The following fields are optional in a Biochemistry object.
if args.name is not None:
biochem['name'] = args.name
if args.description is not None:
biochem['description'] = args.description
# Add the compounds from the compounds file. Required fields: id, name,
# name, abbreviation, formula, defaultCharge, isCofactor
helper = BiochemHelper()
compounds = helper.readCompoundsFile(args.compoundfile, includeLinenum=False)
for index in range(len(compounds)):
biochem['compounds'].append(compounds[index])
# Add the reactions from the reactions file. Required fields: id, name,
# abbreviation, direction, thermoReversibility, status, defaultProtons, reagents.
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
rxn['reagents'] = list()