def parse( self, rxnfile ):
rxnParser = ReactionParser()
result = {} #currently reaction are parsed in an unordered form.
self.startFile(rxnfile)
d = self.getTagedLine()
while d != None:
if d != "":
reaction = rxnParser.parseEquation(d["Equation"])
reaction.setId(d["Name"])
reaction.setName(d["OfficialName"])
reaction.setEquation(d["Equation"])
reaction.annotation = d.annotation
result[d["Name"]] = reaction
d = self.getTagedLine()
self.closeFile()
return result
def __init__( self, delimiter='\t', comment='#' ):
FlatFileParser.__init__( self, delimiter, comment )
self.reactionParser = ReactionParser()
requiredHeaders = {
"Abbreviation":"name",
"Equation":"equation",
"Lower Bound":"lowerBound",
"Upper Bound":"upperBound"
}
optionalHeaders = {"objective":"objective"}
self.addRequiredHeaders( requiredHeaders )
self.addOptionalHeaders( optionalHeaders )
self.setObjectiveTag( "objective function" )
class FluxAnalysisFlatFileParser( FlatFileParser ):
def __init__( self, delimiter='\t', comment='#' ):
FlatFileParser.__init__( self, delimiter, comment )
self.reactionParser = ReactionParser()
requiredHeaders = {
"Abbreviation":"name",
"Equation":"equation",
"Lower Bound":"lowerBound",
"Upper Bound":"upperBound"
}
optionalHeaders = {"objective":"objective"}
self.addRequiredHeaders( requiredHeaders )
self.addOptionalHeaders( optionalHeaders )
self.setObjectiveTag( "objective function" )
def setObjectiveTag( self, objectiveTag ):
self.objectiveTag = objectiveTag
def parseReactionLine( self, line ):
name = line["name"]
equation = line["equation"]
reaction = self.reactionParser.parse( name, "", "", equation )
return reaction
def parseLimitLine( self, line ):
lower = line["lowerBound"]
upper = line["upperBound"]
return ( lower, upper )
def parseObjectiveLine( self, line ):
return -1
def parse( self, analysisFile ):
lines = self.parseFile( analysisFile )
objective = Objective()
limit = FluxLimit()
reactions = {}
for line in lines:
name = line["name"]
reaction = Reaction()
reaction = self.parseReactionLine( line )
reactions[name] = reaction
if line["objective"] == self.objectiveTag:
objectiveValue = self.parseObjectiveLine( line )
objective[name] = objectiveValue
else:
limitValue = self.parseLimitLine( line )
if reaction.direction == 'IRREVERSIBLE-LEFT-TO-RIGHT':
( lower, upper ) = limitValue
limitValue = ( 0.0, upper )
limit[name] = limitValue
return ( reactions, objective, limit )
