keggtools.resolver

Resolve requests to KEGG data Api.

Classes

Resolver

KEGG pathway resolver class.

Functions

get_gene_names(genes[, max_genes])

Resolve KEGG gene identifer to name using to KEGG database REST Api.

Module Contents

class keggtools.resolver.Resolver(cache=None)

KEGG pathway resolver class.

Request interface for KEGG API endpoint.

Parameters:

cache (keggtools.storage.Storage | str | None)

check_organism(organism)

Check if organism code exist.

Parameters:

organism (str) – 3 letter organism code used by KEGG database.

Returns:

Returns True if organism code is found in list of valid organisms.

Return type:

bool

get_compounds(**kwargs)

Get dict of components. Request from KEGG API if not in cache.

Parameters:

kwargs (Any) – other arguments to requests.get.

Returns:

Dict of compound identifier to compound name.

Return type:

Dict[str, str]

get_organism_list(**kwargs)

Get organism codes from file or KEGG API.

Parameters:

kwargs (Any) – other arguments to requests.get.

Returns:

Dict with format {<org>: <org-name>}

Return type:

Dict[str, str]

get_pathway(organism, code, **kwargs)

Load and parse KGML pathway by identifier.

Parameters:

• organism (str) – 3 letter organism code used by KEGG database.

• code (str) – Pathway identify used by KEGG database.

• kwargs (Any) – other arguments to requests.get.

Returns:

Returns parsed Pathway instance.

Return type:

Pathway

get_pathway_list(organism, **kwargs)

Request list of pathways linked to organism.

Parameters:

• organism (str) – 3 letter organism code used by KEGG database.

• kwargs (Any) – other arguments to requests.get.

Returns:

Dict in format {<pathway-id>: <name>}.

Return type:

Dict[str, str]

storage: keggtools.storage.Storage = None

keggtools.resolver.get_gene_names(genes, max_genes=50)

Resolve KEGG gene identifer to name using to KEGG database REST Api.

Function is implemented outside the resolver instance, because requests are not cached and only gene identifier are used.

Parameters:

• genes (List[str]) – List of gene identifer in format “<organism>:<code>”

• max_genes (int)

Returns:

Dict of gene idenifier to gene name.

Return type:

Dict[str, str]