Package Bio :: Package MetaTool :: Module Record
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Source Code for Module Bio.MetaTool.Record

  1  """Hold MetaTool data in a straightforward format. 
  2  """ 
  3   
  4  # standard modules 
  5  import numpy.oldnumeric.matrix as Matrix 
  6   
  7  # local stuff 
  8  import Bio.MetaTool 
  9   
10 -class Metabolite( dict ):
11
12 - def __init__( self, reaction_count, metabolite_name ):
13 self.reaction_count = reaction_count 14 self.metabolite_name = metabolite_name
15
16 - def __str__( self ):
17 out = '%d %s\n' % ( self.reaction_count, self.metabolite_name ) 18 return out
19
20 -class MetaboliteRole( dict ):
21
22 - def __init__( self, met, consumed, built, irreversible_vector ):
23 self.met = met 24 self.consumed = consumed 25 self.built = built 26 self.irreversible_vector = irreversible_vector
27
28 - def __str__( self ):
29 out = '%s\n' % self.met 30 out = out + 'consumed in %d reactions\n' % self.consumed 31 out = out + 'built in %d reactions\n' % self.built 32 out = out + str( self.irreversible_vector ) 33 out = out + '\n' 34 return out
35 36 37
38 -class PathwayTransform:
39
40 - def __init__( self ):
41 self.matrix = None 42 self.enzymes = [] 43 self.reactions = [] 44 self.irreversible_vector = []
45
46 - def __str__( self ):
47 out = '' 48 out = out + '\nMatrix\n' 49 out = out + str( self.matrix ) 50 if( len( self.enzymes ) > 0 ): 51 out = out + '\n Enzymes\n' 52 for enzyme in self.enzymes: 53 out = out + '%s\n' % enzyme 54 if( len( self.reactions ) > 0 ): 55 out = out + '\n Reactions\n' 56 for reaction in self.reactions: 57 out = out + '%s\n' % reaction 58 if( len( self.irreversible_vector ) > 0 ): 59 out = out + '\n\nIrreversible\n\n' 60 for scalar in self.irreversible_vector: 61 out = out + '%03d ' % int( scalar ) 62 out = out + '\n' 63 return out
64 65 66
67 -class Record:
68 69 """Hold MetaTool output information. 70 """ 71
72 - def __init__( self ):
73 self.external_metabolites = [] 74 self.internal_metabolites = [] 75 self.unbalanced_metabolites = [] 76 self.branch_metabolites = [] 77 self.non_branch_metabolites = [] 78 self.sum_is_constant_lines = [] 79 self.stochiometric = PathwayTransform() 80 self.kernel = PathwayTransform() 81 self.subsets = PathwayTransform() 82 self.reduced_system = PathwayTransform() 83 self.convex_basis = PathwayTransform() 84 self.conservation_relations = PathwayTransform() 85 self.elementary_modes = PathwayTransform()
86
87 - def __str__( self ):
88 out = '' 89 out = out + 'Input file name: %s\n' % self.input_file_name 90 out = out + 'Number of internal metabolites: %d\n' % self.num_int_metabolites 91 out = out + 'Number of reactions: %d\n' % self.num_reactions 92 out = out + '\n\nExternal Metabolites\n\ncount name\n\n' 93 for metabolite in self.external_metabolites: 94 out = out + str( metabolite ) 95 out = out + '\n\nInternal Metabolites\n\ncount name\n\n' 96 for metabolite in self.internal_metabolites: 97 out = out + str( metabolite ) 98 out = out + '\n\nBranch Metabolites\n\n' 99 for metabolite in self.branch_metabolites: 100 out = out + str( metabolite ) 101 out = out + '\n\nNon Branch Metabolites\n\n' 102 for metabolite in self.non_branch_metabolites: 103 out = out + str( metabolite ) 104 out = out + '\n\nStochiometric\n\n' 105 out = out + str( self.stochiometric ) 106 if( len( self.unbalanced_metabolites ) > 0 ): 107 out = out + '\n\nUnbalanced Metabolites\n\n' 108 for metabolite in self.unbalanced_metabolites: 109 out = out + '%s\n' % metabolite 110 out = out + '\n\nKernel\n\n' 111 out = out + str( self.kernel ) 112 out = out + '\n\nSubsets\n\n' 113 out = out + str( self.subsets ) 114 out = out + '\n\nReduced System\n\n' 115 out = out + str( self.reduced_system ) 116 out = out + '\n\nConvex Basis\n\n' 117 out = out + str( self.convex_basis ) 118 out = out + '\n\nConservation Relations\n\n' 119 out = out + str( self.conservation_relations ) 120 out = out + '\n' 121 for line in self.sum_is_constant_lines: 122 out = out + '%s\n' % line 123 out = out + '\n\nElementary Modes\n\n' 124 out = out + str( self.elementary_modes ) 125 return out
126