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"""Hold MetaTool data in a straightforward format.
"""
# standard modules
import string
import Matrix
# local stuff
import Bio.MetaTool
class Metabolite( dict ):
def __init__( self, reaction_count, metabolite_name ):
self.reaction_count = reaction_count
self.metabolite_name = metabolite_name
def __str__( self ):
out = '%d %s\n' % ( self.reaction_count, self.metabolite_name )
return out
class MetaboliteRole( dict ):
def __init__( self, met, consumed, built, irreversible_vector ):
self.met = met
self.consumed = consumed
self.built = built
self.irreversible_vector = irreversible_vector
def __str__( self ):
out = '%s\n' % self.met
out = out + 'consumed in %d reactions\n' % self.consumed
out = out + 'built in %d reactions\n' % self.built
out = out + str( self.irreversible_vector )
out = out + '\n'
return out
class PathwayTransform:
def __init__( self ):
self.matrix = None
self.enzymes = []
self.reactions = []
self.irreversible_vector = []
def __str__( self ):
out = ''
out = out + '\nMatrix\n'
out = out + str( self.matrix )
if( len( self.enzymes ) > 0 ):
out = out + '\n Enzymes\n'
for enzyme in self.enzymes:
out = out + '%s\n' % enzyme
if( len( self.reactions ) > 0 ):
out = out + '\n Reactions\n'
for reaction in self.reactions:
out = out + '%s\n' % reaction
if( len( self.irreversible_vector ) > 0 ):
out = out + '\n\nIrreversible\n\n'
for scalar in self.irreversible_vector:
out = out + '%03d ' % int( scalar )
out = out + '\n'
return out
class Record:
"""Hold MetaTool output information.
"""
def __init__( self ):
self.external_metabolites = []
self.internal_metabolites = []
self.unbalanced_metabolites = []
self.branch_metabolites = []
self.non_branch_metabolites = []
self.sum_is_constant_lines = []
self.stochiometric = PathwayTransform()
self.kernel = PathwayTransform()
self.subsets = PathwayTransform()
self.reduced_system = PathwayTransform()
self.convex_basis = PathwayTransform()
self.conservation_relations = PathwayTransform()
self.elementary_modes = PathwayTransform()
def __str__( self ):
out = ''
out = out + 'Input file name: %s\n' % self.input_file_name
out = out + 'Number of internal metabolites: %d\n' % self.num_int_metabolites
out = out + 'Number of reactions: %d\n' % self.num_reactions
out = out + '\n\nExternal Metabolites\n\ncount name\n\n'
for metabolite in self.external_metabolites:
out = out + str( metabolite )
out = out + '\n\nInternal Metabolites\n\ncount name\n\n'
for metabolite in self.internal_metabolites:
out = out + str( metabolite )
out = out + '\n\nBranch Metabolites\n\n'
for metabolite in self.branch_metabolites:
out = out + str( metabolite )
out = out + '\n\nNon Branch Metabolites\n\n'
for metabolite in self.non_branch_metabolites:
out = out + str( metabolite )
out = out + '\n\nStochiometric\n\n'
out = out + str( self.stochiometric )
if( len( self.unbalanced_metabolites ) > 0 ):
out = out + '\n\nUnbalanced Metabolites\n\n'
for metabolite in self.unbalanced_metabolites:
out = out + '%s\n' % metabolite
out = out + '\n\nKernel\n\n'
out = out + str( self.kernel )
out = out + '\n\nSubsets\n\n'
out = out + str( self.subsets )
out = out + '\n\nReduced System\n\n'
out = out + str( self.reduced_system )
out = out + '\n\nConvex Basis\n\n'
out = out + str( self.convex_basis )
out = out + '\n\nConservation Relations\n\n'
out = out + str( self.conservation_relations )
out = out + '\n'
for line in self.sum_is_constant_lines:
out = out + '%s\n' % line
out = out + '\n\nElementary Modes\n\n'
out = out + str( self.elementary_modes )
return out
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