Documentation
¶
Overview ¶
Package ncbiprotein is the library behind the ncbiprotein command line: the HTTP client, request shaping, and the typed data models for NCBI Protein.
The Client here is the spine every command shares. It sets a real User-Agent, paces requests so a busy session stays polite, and retries the transient failures (429 and 5xx) that any public API throws under load. 1.6 billion protein sequence records, no API key required.
Index ¶
- Constants
- type Client
- func (c *Client) FetchProteins(ctx context.Context, ids []string) ([]*Protein, error)
- func (c *Client) GetProtein(ctx context.Context, uid string) (*Protein, error)
- func (c *Client) Search(ctx context.Context, query string, limit, start int) ([]string, int, error)
- func (c *Client) SearchAndFetch(ctx context.Context, query string, limit, start int) ([]*Protein, int, error)
- type Config
- type Domain
- type Protein
Constants ¶
const Host = "eutils.ncbi.nlm.nih.gov"
Host is the eUtils hostname this client talks to, and the host the URI driver in domain.go claims.
Variables ¶
This section is empty.
Functions ¶
This section is empty.
Types ¶
type Client ¶
type Client struct {
// contains filtered or unexported fields
}
Client talks to NCBI eUtils for protein records.
func (*Client) FetchProteins ¶
FetchProteins fetches protein details for the given IDs (up to ~500 per call; callers should batch if needed).
func (*Client) GetProtein ¶
GetProtein fetches a single protein by its NCBI numeric UID or accession.
type Config ¶
type Config struct {
BaseURL string
Rate time.Duration
Retries int
Timeout time.Duration
UserAgent string
}
Config holds the runtime settings for the ncbiprotein client.
func DefaultConfig ¶
func DefaultConfig() Config
DefaultConfig returns a Config with sensible defaults: 400ms rate limit, 3 retries, and a 30s timeout.
type Domain ¶
type Domain struct{}
Domain is the ncbiprotein driver. It carries no state; the per-run client is built by the factory Register hands kit.
func (Domain) Classify ¶
Classify turns any accepted input into the canonical (type, id). Any non-empty string is accepted as a protein UID or accession.
func (Domain) Info ¶
func (Domain) Info() kit.DomainInfo
Info describes the scheme, the hostnames a pasted link is matched against, and the identity reused for the binary's help and version.
type Protein ¶
type Protein struct {
ID string `json:"id" kit:"id"`
Accession string `json:"accession"`
Title string `json:"title"`
TaxID int `json:"tax_id,omitempty"`
Length int `json:"length,omitempty"`
MolType string `json:"mol_type,omitempty"`
SourceDB string `json:"source_db,omitempty"`
Completeness string `json:"completeness,omitempty"`
CreateDate string `json:"create_date,omitempty"`
UpdateDate string `json:"update_date,omitempty"`
}
Protein is a single NCBI Protein sequence record.
Source Files