cocomico.report

Generate reports for communities, using results that are already computed.

Functions

write_json(communities, output_dir[, mode])

Write a JSON-formatted file of computed results for each member of

from_community(→ str)

Serialize a community and optionally any results computed for it.

to_json(→ str)

Serialize a cocomico object and convert to JSON string.

write_tabular(communities, output_file[, mode, ...])

Write CSV-formatted table of computed results for a collection of

read_tabular(output_file[, mode, dialect])

Read CSV-formatted table of computed results.

serializer(object_type)

Decorator to register serializers by name.

lookup_serializer(coco)

Look up the serializer by type name.

serialize(coco, *args, **kwargs)

Dispatch serialization based on object type

serialize_number(obj)

Number do not need conversion.

serialize_str(obj)

Convert an object that has a __str__ method.

serialize_iterable(obj[, sort])

Convert iterable object.

serialize_dict(obj)

Convert dict object.

serialize_seeds(→ list[str])

Convert seeds.

serialize_metaboliteset(→ list[str])

Convert set of metabolites.

serialize_model(→ list)

Convert model.

serialize_exchange(→ list)

Convert set of metabolites.

serialize_community(→ dict)

Convert community. Ensure that the taxa and models lists are in the same order.

serialize_results(→ list)

Convert community analyses.

Module Contents

cocomico.report.write_json(communities: Dict[str, cocomico.community.Community], output_dir: pathlib.Path, mode: str = 'w+')[source]

Write a JSON-formatted file of computed results for each member of a collection of communities.

Parameters:
cocomico.report.from_community(community: cocomico.community.Community, with_results: bool = True, seeds_todo: Iterable[cocomico.base.Seeds] | None = None) → str[source]

Serialize a community and optionally any results computed for it.

Parameters:
Return type:

str

cocomico.report.to_json(payload: object) → str[source]

Serialize a cocomico object and convert to JSON string.

Parameters:

payload (object)

Return type:

str

cocomico.report.write_tabular(communities: Dict[str, cocomico.community.Community], output_file: pathlib.Path, mode: str = 'w', dialect='excel-tab', header=True, symbolic_seeds=False, seeds_todo: Iterable[cocomico.base.Seeds] | None = None)[source]

Write CSV-formatted table of computed results for a collection of communities.

Parameters:
cocomico.report.read_tabular(output_file: pathlib.Path, mode: str = 'r', dialect='excel-tab')[source]

Read CSV-formatted table of computed results.

Parameters:

  • output_file (pathlib.Path)

  • mode (str)

cocomico.report.serializer(object_type: str)[source]

Decorator to register serializers by name.

Parameters:

object_type (str)

cocomico.report.lookup_serializer(coco: object)[source]

Look up the serializer by type name.

Parameters:

coco (object)

cocomico.report.serialize(coco: object, *args, **kwargs)[source]

Dispatch serialization based on object type

Parameters:

coco (object)

cocomico.report.serialize_number(obj)[source]

Number do not need conversion.

cocomico.report.serialize_str(obj)[source]

Convert an object that has a __str__ method.

cocomico.report.serialize_iterable(obj: Iterable, sort=True)[source]

Convert iterable object.

Parameters:

obj (Iterable)

cocomico.report.serialize_dict(obj: dict)[source]

Convert dict object.

Parameters:

obj (dict)

cocomico.report.serialize_seeds(seeds: cocomico.base.Seeds) → list[str][source]

Convert seeds.

Parameters:

seeds (cocomico.base.Seeds)

Return type:

list[str]

cocomico.report.serialize_metaboliteset(metaboliteset: cocomico.base.MetaboliteSet) → list[str][source]

Convert set of metabolites.

Parameters:

metaboliteset (cocomico.base.MetaboliteSet)

Return type:

list[str]

cocomico.report.serialize_model(model: cocomico.model.Model) → list[source]

Convert model.

Parameters:

model (cocomico.model.Model)

Return type:

list

cocomico.report.serialize_exchange(exchange: cocomico.base.Exchange) → list[source]

Convert set of metabolites.

Parameters:

exchange (cocomico.base.Exchange)

Return type:

list

cocomico.report.serialize_community(community: cocomico.community.Community) → dict[source]

Convert community. Ensure that the taxa and models lists are in the same order.

Parameters:

community (cocomico.community.Community)

Return type:

dict

cocomico.report.serialize_results(community: cocomico.community.Community) → list[source]

Convert community analyses.

Parameters:

community (cocomico.community.Community)

Return type:

list