cocomico.cwl

CoCoMiCo cwl endpoint.

Functions

entrypoint(ctx[, seeds_file, seeds_def, sbml_dir, ...])

Perform CoCoMiCo analyses for communities, with respect to seeds.

community(ctx[, output, seeds_file, seeds_def, ...])

CoCoMiCo for a community defined by the MODELs, or by all models in sbml_dir.

find_specs(→ Iterable[Tuple[str, ...)

Find all communities in given spec files or directories of

specification(ctx, spec, argspec[, output, ...])

CoCoMiCo for all communities defined by a specification file.

example(ctx, output[, header_csv])

CoCoMiCo for a small example community.

process_communities(seeds_todo, communities[, output, ...])

Analyze each community with respect to every set of seeds.

retrieve_seeds(→ list[cocomico.base.Seeds])

Combine seeds specified in an SBML file and seeds specified in-line

Module Contents

cocomico.cwl.entrypoint(ctx: click.Context, seeds_file: List[pathlib.Path] | None = None, seeds_def: List[str] | None = None, sbml_dir: pathlib.Path | None = None, output: pathlib.Path | None = None, csv_output: pathlib.Path | None = None, header_csv: bool = True, name: str = 'community', loglevel: str = 'INFO', symbolic_seeds: bool = False, ignore_seed_reactions: bool = False)

Perform CoCoMiCo analyses for communities, with respect to seeds.

cocomico community
    --seeds-file seeds.sbml
    --json-output results.json
    --csv-output results.csv
    sbml/Com2Org*.sbml
Parameters:

  • ctx (click.Context)

  • seeds_file (List[pathlib.Path] | None)

  • seeds_def (List[str] | None)

  • sbml_dir (pathlib.Path | None)

  • output (pathlib.Path | None)

  • csv_output (pathlib.Path | None)

  • header_csv (bool)

  • name (str)

  • loglevel (str)

  • symbolic_seeds (bool)

  • ignore_seed_reactions (bool)

cocomico.cwl.community(ctx: click.Context, output: pathlib.Path | None = None, seeds_file: List[pathlib.Path] | None = None, seeds_def: List[str] | None = None, sbml_dir: pathlib.Path | None = None, csv_output: pathlib.Path | None = None, header_csv: bool = True, name: str = 'community', json_output: pathlib.Path | None = None, model: Iterable[pathlib.Path] | None = None)

CoCoMiCo for a community defined by the MODELs, or by all models in sbml_dir.

cocomico community
    --seeds-def M_E_c,M_F_c,M_X1_c
    --seeds-file seeds.sbml
    --json-output results.json
    --csv-output results.csv
    sbml/Com2Org*.sbml
Parameters:

  • ctx (click.Context)

  • output (pathlib.Path | None)

  • seeds_file (List[pathlib.Path] | None)

  • seeds_def (List[str] | None)

  • sbml_dir (pathlib.Path | None)

  • csv_output (pathlib.Path | None)

  • header_csv (bool)

  • name (str)

  • json_output (pathlib.Path | None)

  • model (Iterable[pathlib.Path] | None)

cocomico.cwl.find_specs(paths: Iterable[pathlib.Path], sbml_dir: pathlib.Path) → Iterable[Tuple[str, cocomico.community.Community]][source]

Find all communities in given spec files or directories of spec files.

Parameters:

  • paths (Iterable[pathlib.Path])

  • sbml_dir (pathlib.Path)

Return type:

Iterable[Tuple[str, cocomico.community.Community]]

cocomico.cwl.specification(ctx: click.Context, spec: List[pathlib.Path], argspec: List[pathlib.Path], output: pathlib.Path | None = None, seeds_file: List[pathlib.Path] | None = None, seeds_def: List[str] | None = None, sbml_dir: pathlib.Path | None = None, csv_output: pathlib.Path | None = None, header_csv: bool = True)

CoCoMiCo for all communities defined by a specification file.

cocomico spec
    --spec communities.json
    --seeds-file seeds.sbml
    --output results
Parameters:

  • ctx (click.Context)

  • spec (List[pathlib.Path])

  • argspec (List[pathlib.Path])

  • output (pathlib.Path | None)

  • seeds_file (List[pathlib.Path] | None)

  • seeds_def (List[str] | None)

  • sbml_dir (pathlib.Path | None)

  • csv_output (pathlib.Path | None)

  • header_csv (bool)

cocomico.cwl.example(ctx: click.Context, output: pathlib.Path, header_csv: bool = True)

CoCoMiCo for a small example community.

 cocomico example –output results

Parameters:

  • ctx (click.Context)

  • output (pathlib.Path)

  • header_csv (bool)

cocomico.cwl.process_communities(seeds_todo: Iterable[cocomico.base.Seeds], communities: dict[str, cocomico.community.Community], output: pathlib.Path | None = None, json_output: dict[str, pathlib.Path | None] | None = None, csv_output: pathlib.Path | None = None, header_csv: bool = True, symbolic_seeds: bool = False)[source]

Analyze each community with respect to every set of seeds.

Parameters:

  • seeds_todo (Iterable[cocomico.base.Seeds])

  • communities (dict[str, cocomico.community.Community])

  • output (pathlib.Path | None)

  • json_output (dict[str, pathlib.Path | None] | None)

  • csv_output (pathlib.Path | None)

  • header_csv (bool)

  • symbolic_seeds (bool)

cocomico.cwl.retrieve_seeds(seeds_file: Sequence[pathlib.Path] | None = None, seeds_def: Sequence[str] | None = None) → list[cocomico.base.Seeds][source]

Combine seeds specified in an SBML file and seeds specified in-line as comma-separated strings. May be empty: the group-level seeds option is often unspecified.

Parameters:

  • seeds_file (Sequence[pathlib.Path] | None)

  • seeds_def (Sequence[str] | None)

Return type:

list[cocomico.base.Seeds]