go
Module for Gene Ontology (GO) functions.
Aspect = Literal['cellular_component', 'biological_process', 'molecular_function']
module-attribute
The aspect of the GO term.
allowed_aspects = set(get_args(Aspect))
module-attribute
Allowed aspects for GO terms.
GoTerm
dataclass
A Gene Ontology (GO) term.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
id
|
str
|
The unique identifier for the GO term, e.g., 'GO:0043293'. |
required |
is_obsolete
|
bool
|
Whether the GO term is obsolete. |
required |
name
|
str
|
The name of the GO term. |
required |
definition
|
str
|
The definition of the GO term. |
required |
aspect
|
Aspect
|
The aspect of the GO term. |
required |
search_gene_ontology_term(term, aspect=None, include_obsolete=False, limit=100)
async
Search for a Gene Ontology (GO) term by its name or ID.
Calls the EBI QuickGO API at https://www.ebi.ac.uk/QuickGO/api/index.html .
Examples:
To search for apoptosome terms do.
>>> from protein_quest.go import search_go_term
>>> r = await search_go_term('apoptosome')
>>> len(r)
5
>>> r[0]
GoTerm(id='GO:0043293', is_obsolete=False, name='apoptosome', definition='A multisubunit protein ...')
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
term
|
str
|
The GO term to search for. For example |
required |
aspect
|
Aspect | None
|
The aspect to filter by. If not given, all aspects are included. |
None
|
include_obsolete
|
bool
|
Whether to include obsolete terms. By default, obsolete terms are excluded. |
False
|
limit
|
int
|
The maximum number of results to return. |
100
|
Returns:
| Type | Description |
|---|---|
list[GoTerm]
|
List of GO terms |
Raises:
| Type | Description |
|---|---|
ValueError
|
If the aspect is invalid. |
write_go_terms_to_csv(terms, csv_file)
Write a list of GO terms to a CSV file.
Parameters:
| Name | Type | Description | Default |
|---|---|---|---|
terms
|
list[GoTerm]
|
The list of GO terms to write. |
required |
csv_file
|
TextIOWrapper
|
The CSV file to write to. |
required |