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 string 
  6   
  7  import Matrix 
  8   
  9  # local stuff 
 10  import Bio.MetaTool 
 11   
12 -class Metabolite( dict ):
13
14 - def __init__( self, reaction_count, metabolite_name ):
15 self.reaction_count = reaction_count 16 self.metabolite_name = metabolite_name
17
18 - def __str__( self ):
19 out = '%d %s\n' % ( self.reaction_count, self.metabolite_name ) 20 return out
21
22 -class MetaboliteRole( dict ):
23
24 - def __init__( self, met, consumed, built, irreversible_vector ):
25 self.met = met 26 self.consumed = consumed 27 self.built = built 28 self.irreversible_vector = irreversible_vector
29
30 - def __str__( self ):
31 out = '%s\n' % self.met 32 out = out + 'consumed in %d reactions\n' % self.consumed 33 out = out + 'built in %d reactions\n' % self.built 34 out = out + str( self.irreversible_vector ) 35 out = out + '\n' 36 return out
37 38 39
40 -class PathwayTransform:
41
42 - def __init__( self ):
43 self.matrix = None 44 self.enzymes = [] 45 self.reactions = [] 46 self.irreversible_vector = []
47
48 - def __str__( self ):
49 out = '' 50 out = out + '\nMatrix\n' 51 out = out + str( self.matrix ) 52 if( len( self.enzymes ) > 0 ): 53 out = out + '\n Enzymes\n' 54 for enzyme in self.enzymes: 55 out = out + '%s\n' % enzyme 56 if( len( self.reactions ) > 0 ): 57 out = out + '\n Reactions\n' 58 for reaction in self.reactions: 59 out = out + '%s\n' % reaction 60 if( len( self.irreversible_vector ) > 0 ): 61 out = out + '\n\nIrreversible\n\n' 62 for scalar in self.irreversible_vector: 63 out = out + '%03d ' % int( scalar ) 64 out = out + '\n' 65 return out
66 67 68
69 -class Record:
70 71 """Hold MetaTool output information. 72 """ 73
74 - def __init__( self ):
75 self.external_metabolites = [] 76 self.internal_metabolites = [] 77 self.unbalanced_metabolites = [] 78 self.branch_metabolites = [] 79 self.non_branch_metabolites = [] 80 self.sum_is_constant_lines = [] 81 self.stochiometric = PathwayTransform() 82 self.kernel = PathwayTransform() 83 self.subsets = PathwayTransform() 84 self.reduced_system = PathwayTransform() 85 self.convex_basis = PathwayTransform() 86 self.conservation_relations = PathwayTransform() 87 self.elementary_modes = PathwayTransform()
88
89 - def __str__( self ):
90 out = '' 91 out = out + 'Input file name: %s\n' % self.input_file_name 92 out = out + 'Number of internal metabolites: %d\n' % self.num_int_metabolites 93 out = out + 'Number of reactions: %d\n' % self.num_reactions 94 out = out + '\n\nExternal Metabolites\n\ncount name\n\n' 95 for metabolite in self.external_metabolites: 96 out = out + str( metabolite ) 97 out = out + '\n\nInternal Metabolites\n\ncount name\n\n' 98 for metabolite in self.internal_metabolites: 99 out = out + str( metabolite ) 100 out = out + '\n\nBranch Metabolites\n\n' 101 for metabolite in self.branch_metabolites: 102 out = out + str( metabolite ) 103 out = out + '\n\nNon Branch Metabolites\n\n' 104 for metabolite in self.non_branch_metabolites: 105 out = out + str( metabolite ) 106 out = out + '\n\nStochiometric\n\n' 107 out = out + str( self.stochiometric ) 108 if( len( self.unbalanced_metabolites ) > 0 ): 109 out = out + '\n\nUnbalanced Metabolites\n\n' 110 for metabolite in self.unbalanced_metabolites: 111 out = out + '%s\n' % metabolite 112 out = out + '\n\nKernel\n\n' 113 out = out + str( self.kernel ) 114 out = out + '\n\nSubsets\n\n' 115 out = out + str( self.subsets ) 116 out = out + '\n\nReduced System\n\n' 117 out = out + str( self.reduced_system ) 118 out = out + '\n\nConvex Basis\n\n' 119 out = out + str( self.convex_basis ) 120 out = out + '\n\nConservation Relations\n\n' 121 out = out + str( self.conservation_relations ) 122 out = out + '\n' 123 for line in self.sum_is_constant_lines: 124 out = out + '%s\n' % line 125 out = out + '\n\nElementary Modes\n\n' 126 out = out + str( self.elementary_modes ) 127 return out
128