silvio.extensions package

Subpackages

• silvio.extensions.modules package
  • Submodules
  • silvio.extensions.modules.genome_expression module
  • silvio.extensions.modules.genome_library module
  • silvio.extensions.modules.genome_list module
  • silvio.extensions.modules.growth_behaviour module
  • silvio.extensions.modules.metabolic_flux module
  • silvio.extensions.modules.phenotype_size module
• silvio.extensions.records package
  • Subpackages
    • silvio.extensions.records.gene package
      • Submodules
      • silvio.extensions.records.gene.crafted_gene module
      • silvio.extensions.records.gene.gene module
      • silvio.extensions.records.gene.localized_gene module
      • silvio.extensions.records.gene.stub_gene module
  • Submodules
  • silvio.extensions.records.growth_record module
• silvio.extensions.sets package
  • Subpackages
    • silvio.extensions.sets.shotgun_sequencing package
      • Submodules
      • silvio.extensions.sets.shotgun_sequencing.assembly module
      • silvio.extensions.sets.shotgun_sequencing.datatype module
      • silvio.extensions.sets.shotgun_sequencing.evaluation module
      • silvio.extensions.sets.shotgun_sequencing.sequencing module
      • silvio.extensions.sets.shotgun_sequencing.storage module
      • silvio.extensions.sets.shotgun_sequencing.visualization module
• silvio.extensions.tools package
  • Submodules
  • silvio.extensions.tools.shotgun_sequencing module
• silvio.extensions.utils package
  • Submodules
  • silvio.extensions.utils.laboratory module
  • silvio.extensions.utils.misc module
  • silvio.extensions.utils.shotgun_sequencing module
  • silvio.extensions.utils.transform module
  • silvio.extensions.utils.visual module

Submodules

silvio.extensions.all_events module

class silvio.extensions.all_events.AlterGeneExpressionEvent(gene: silvio.extensions.records.gene.gene.Gene, new_expression: float)

Bases: silvio.events.Event

_abc_impl = <_abc._abc_data object>

class silvio.extensions.all_events.AlterGenePromoterEvent(gene: silvio.extensions.records.gene.gene.Gene, new_promoter: Bio.Seq.Seq)

Bases: silvio.events.Event

_abc_impl = <_abc._abc_data object>

class silvio.extensions.all_events.InsertGeneEvent(gene: silvio.extensions.records.gene.gene.Gene, locus: Optional[int])

Bases: silvio.events.Event

_abc_impl = <_abc._abc_data object>

class silvio.extensions.all_events.RemoveGeneEvent(gene: silvio.extensions.records.gene.gene.Gene)

Bases: silvio.events.Event

_abc_impl = <_abc._abc_data object>

silvio.extensions.common module

Common datatypes between the different extensions.