Curation (Python)¶

raven-toolbox objects in raven_toolbox.curation, collected from the source of the tracked branch.

Functions¶

Function	Summary
`batch_curate`	Add or update metabolites / reactions / genes from data tables.
`batch_curate_from_tsv`	File-path convenience wrapper for :func:`batch_curate`.
`CurationResult`	Record of what :func:`batch_curate` added / updated.

Reference¶

batch_curate¶

Add or update metabolites / reactions / genes from data tables.

Each table is optional. rxns_df and rxns_coeffs_df must be provided together (one describes the per-reaction attributes, the other carries the stoichiometric coefficients).

Parameters:

Name	Type	Description	Default
`model`	`Model`	Model to curate in place.	required
`mets_df`	`DataFrame \| None`	Tables matching the schema described in :mod:`raven_toolbox.curation`.	`None`
`genes_df`	`DataFrame \| None`	Tables matching the schema described in :mod:`raven_toolbox.curation`.	`None`
`rxns_df`	`DataFrame \| None`	Tables matching the schema described in :mod:`raven_toolbox.curation`.	`None`
`rxns_coeffs_df`	`DataFrame \| None`	Tables matching the schema described in :mod:`raven_toolbox.curation`.	`None`
`met_id_prefix`	`str`	Prefixes for freshly-generated metabolite / reaction ids (e.g. `s_` and `r_` for yeast-GEM, `M_` and `R_` for the cobrapy / BiGG default). New entity ids are formed by finding the largest existing zero-padded suffix matching the prefix and incrementing from there.	`'M_'`
`rxn_id_prefix`	`str`	Prefixes for freshly-generated metabolite / reaction ids (e.g. `s_` and `r_` for yeast-GEM, `M_` and `R_` for the cobrapy / BiGG default). New entity ids are formed by finding the largest existing zero-padded suffix matching the prefix and incrementing from there.	`'M_'`

Returns:

Name	Type	Description
`A`	class:`CurationResult` summarising the changes.

batch_curate_from_tsv¶

File-path convenience wrapper for :func:batch_curate.

Each path is optional. TSVs are read with pandas' default read_csv(sep='\t'); empty cells become NaN (not the empty string), which the engine treats as "skip this field".

CurationResult¶

Record of what :func:batch_curate added / updated.

Each list holds the cobra ids of the affected entities, in the order they were processed.