Methods module

This module is divided into two parts. The first contains the gapfilling methods, which are used to fill gaps in the metabolic network. The second part contains the reconstruction methods, which are used to reconstruct the metabolic network from the omics data.

• Gapfilling Methods
  • Combinatorial Gapfilling Algorithm
    • CombinatorialGapfill
  • Elementary Flux Mode Gapfilling Algorithm
    • EFMGapfill
    • EFMGapfillProperties
  • FastCC Gapfilling Algorithm
    • FastCC
    • FastCCProperties
  • Pathway Analysis Gapfilling Algorithm
    • CombinatorialEFMGapfill
    • SubEFMGapfill
    • simulate_context()
• Reconstruction Methods
  • Corda Algorithm
    • CORDA
    • CORDAProperties
    • CORSOModel
    • CORSOSolution
  • FastCORE Algorithm
    • FASTcore
    • FastcoreProperties
  • GIMME Algorithm
    • GIMME
    • GIMMEModel
    • GIMMEProperties
    • GIMMESolution
  • iMAT Algorithm
    • IMAT
    • IMATProperties
  • SwiftCore Algorithm
    • SWIFTCORE
    • SwiftcoreProperties
    • find_core()
  • (t)INIT Algorithm
    • tINIT
    • tINITProperties

Base classes for Gapfilling and Reconstruction

class troppo.methods.base.ContextSpecificModelReconstructionAlgorithm(S, lb, ub, properties)

Bases: object

property properties_class

abstract run()

class troppo.methods.base.GapfillAlgorithm(S, lb, ub, properties)

Bases: object

property properties_class

abstract run()

class troppo.methods.base.GapfillProperties

Bases: PropertyDictionary

This class is used to define the properties of the gap-filling algorithms.

Parameters

base_mandatorydict

Dictionary containing the mandatory properties of the gap-filling algorithm. Includes: solver.

base_optionaldict

Dictionary containing the optional properties of the gap-filling algorithm. Includes: lsystem_args, avbl_fluxes.

decoder_function = {'avbl_fluxes': <function decode_rx_list>, 'lsystem_args': <function GapfillProperties.<lambda>>}

class troppo.methods.base.PropertiesReconstruction

Bases: PropertyDictionary

This class is used to define the properties of the reconstruction algorithm.

Parameters

base_mandatorydict

Dictionary containing the mandatory properties of the reconstruction algorithm. Includes: solver, template_model, omics_type.

base_optionaldict

Dictionary containing the optional properties of the reconstruction algorithm. Includes: env_conditions, flux_threshold.

abstract static from_integrated_scores(scores, **kwargs)

troppo.methods.base.decode_mt_list(x, rx, mt)

troppo.methods.base.decode_rx_list(x, rx, mt)