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tasks_and_gapfilling.md

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Metabolic tasks & gap-filling

Tasks — {mod}raven_toolbox.tasks

A metabolic task asserts that a model can (or cannot) produce/consume a set of metabolites under given constraints.

  • {class}raven_toolbox.tasks.Task + {func}raven_toolbox.tasks.parse_task_list — the task-list file format.
  • {func}raven_toolbox.tasks.check_tasks + {class}raven_toolbox.tasks.TaskResult — run tasks against a model. check_tasks reuses one model across the whole list (no per-task model copy) — at genome scale ~12× faster than a copy-per-task implementation.
  • {func}raven_toolbox.tasks.find_task_essential_reactions — the reactions a model must use to satisfy a task list. This is the input to (f)tINIT's task layer (see the context-specific modeling guide).

Connectivity gap-filling — {mod}raven_toolbox.gapfilling

{func}raven_toolbox.gapfilling.connect_blocked_reactions adds the fewest (lowest-penalty) template reactions so reactions that are blocked in a draft can carry flux — the connectivity flavour of RAVEN's fillGaps.

:::{tip} For the other flavour — add reactions until a specific objective becomes feasible — use cobra's {func}cobra.flux_analysis.gapfill directly. :::