napistu.modify.curation
Functions
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Curate SBML_dfs |
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Format Curated Entities |
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Format Curations |
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Read Pathway Curations |
- napistu.modify.curation._add_entity_foreign_keys(new_curated_entities: DataFrame, entity_type: str, type_schema: dict[str, Any], new_entities: dict[str, DataFrame], sbml_dfs: SBML_dfs) DataFrame
Add foreign key columns to curated entities.
- napistu.modify.curation._add_entity_identifiers(new_curated_entities: DataFrame, type_schema: dict[str, Any]) DataFrame
Add identifier column to curated entities.
- napistu.modify.curation._add_entity_labels(new_curated_entities: DataFrame, entity_type: str, type_schema: dict[str, Any]) DataFrame
Add label column to curated entities.
- napistu.modify.curation._add_entity_primary_keys(new_curated_entities: DataFrame, entity_type: str, type_schema: dict[str, Any], sbml_dfs: SBML_dfs) DataFrame
Add primary key column to curated entities.
- napistu.modify.curation._add_entity_sources(new_curated_entities: DataFrame, type_schema: dict[str, Any], curation_id: str) DataFrame
Add source column to curated entities.
- napistu.modify.curation._expand_entities_by_fks(sbml_dfs: SBML_dfs, pk_dict: dict) dict
Expand Entities By Foreign Keys
Starting with a dictionary of foreign keys, add all primary keys that are defined by these foreign keys
Params
- sbml_dfs: SBML_dfs
A pathway model
- pk_dict: dict
Dictionary where keys are types of primary keys in sbml_dfs
- returns:
pk_dict – Input where additional primary keys may have been added
- rtype:
dict
- napistu.modify.curation._find_invalid_entities(sbml_dfs: SBML_dfs, invalid_entities: DataFrame) dict[str, set]
Find Invalid Entities
Based on a set of entity names or attributes, find each entities corresponding primary key
Params
- sbml_dfs: SBML_dfs
A pathway model
- invalid_entities: pd.DataFrame
A table containing entities to be removed (“remove”), the table where the entity resides (“table”) and variable used to find the entity (“variable”)
- returns:
invalid_entities_dict – A dictionary containing the primary keys of invalid entities
- rtype:
dict
- napistu.modify.curation._format_explicit_reaction_species(curation_dict: dict[str, DataFrame]) DataFrame | None
Format reaction species which are deirectly defined among curated species.
- napistu.modify.curation._format_implicit_reaction_species(curation_dict: dict[str, DataFrame]) DataFrame
Construct reaction species which are defined in reactions’ stoichiometry.
- napistu.modify.curation._remove_entities(sbml_dfs: SBML_dfs, pk_dict: dict) SBML_dfs
Remove Entities
Remove entities whose primary keys are in pk_dict
Params
- sbml_dfs: SBML_dfs
A pathway model
- pk_dict: dict
Dictionary where keys are types of primary keys in sbml_dfs
- returns:
sbml_dfs – Input with some entities removed
- rtype:
SBML_dfs
- napistu.modify.curation._validate_format_curated_entities_inputs(entity_type: str, new_curated_entities: DataFrame, new_entities: dict[str, DataFrame], sbml_dfs: SBML_dfs, curation_id: str) None
Validate inputs for format_curated_entities.
- napistu.modify.curation.curate_sbml_dfs(curation_dir: str, sbml_dfs: SBML_dfs, verbose: bool = True) SBML_dfs
Curate SBML_dfs
Update a pathway model using manual annotations.
The current workflow is to: - annotate pathways in https://docs.google.com/spreadsheets/d/1waVXSVMOthL5QAT0PITgLMDdXGHIS50LZ2P1_F_c-6s/edit#gid=101210748 - parse annotations into flat files using parse_manual_annotation.Rmd - call this function to format flat files and update a current SBML_dfs pathway model
Params
- curation_dir: str
Directory containing annotations generated using parse_manual_annotation.Rmd
- sbml_dfs: SBML_dfs
A pathway model
- verbose: bool
Extra reporting
- returns:
sbml_df – A curated pathway model
- rtype:
SBML_dfs
- napistu.modify.curation.format_curated_entities(entity_type: str, new_curated_entities: dict[Any, DataFrame], new_entities: dict[str, DataFrame], sbml_dfs: SBML_dfs, curation_id: str = 'Calico curations') DataFrame
Format Curated Entities
Convert entities from the curation format to the stucture of SBML_dfs tables
Params
- entity_type: str
The type of entity to update (e.g., reactions, species, …)
- new_curated_entities: dict
Curation pd.DataFrames generated using read_pathway_curations
- new_entities: dict
Curations formatted as SBML_dfs tables
- sbml_dfs: SBML_dfs
A pathway model
- curation_id: str
Name to use as a pathway id in Source objects
- returns:
new_entity_df – Input for entity_type formatted as an SBML_dfs table
- rtype:
pd.DataFrame
- napistu.modify.curation.format_curations(curation_dict: dict[str, DataFrame], sbml_dfs: SBML_dfs) dict[str, DataFrame]
Format Curations
Format manual curations into a set of table that can be appended to an sbml_dfs’s tables
Params
- curation_dict:
Curations imported using read_pathway_curations
- sbml_dfs:
A pathway model
- returns:
new_entities – Curations formatted as SBML_dfs tables
- rtype:
dict
- napistu.modify.curation.read_pathway_curations(curation_dir: str) dict[str, DataFrame]
Read Pathway Curations
Load curations that were prepared by parse_manual_annotations.Rmd
Params
- curation_dir: str
Directory containing annotations generated using parse_manual_annotation.Rmd
- returns:
curations – Dictionary containing different types of annoations
- rtype:
dict