Getting started with KEGGAPI.jl

Installation

From the Julia REPL, type ] to enter the Pkg REPL and install KEGGAPI.jl:

pkg> add KEGGAPI

Usage

Load KEGGAPI.jl with using:

Each wrapper is named after its KEGG operation. This call lists all organisms in KEGG:

result = KEGGAPI.kegg_list("genome")
@assert result isa KEGGAPI.KeggTupleList

The result contains the request URL, column names, and data:

result.url

"https://rest.kegg.jp/list/genome"

result.colnames

2-element Vector{Union{Missing, String}}:
 "ID"
 missing

result.data

11951-element Vector{Any}:
 ["T01001", "hsa; Homo sapiens (human)"]
 ["T01005", "ptr; Pan troglodytes (chimpanzee)"]
 ["T02283", "pps; Pan paniscus (bonobo)"]
 ["T02442", "ggo; Gorilla gorilla gorilla (western lowland gorilla)"]
 ["T01416", "pon; Pongo abelii (Sumatran orangutan)"]
 ["T10128", "ppyg; Pongo pygmaeus (Bornean orangutan)"]
 ["T03265", "nle; Nomascus leucogenys (northern white-cheeked gibbon)"]
 ["T08803", "hmh; Hylobates moloch (silvery gibbon)"]
 ["T10134", "ssyn; Symphalangus syndactylus (siamang)"]
 ["T01028", "mcc; Macaca mulatta (rhesus monkey)"]
 ⋮
 ["T10160", "nocc; Candidatus Nanohalococcus occultus"]
 ["T10381", "nhf; Candidatus Nanohalovita haloferacivicina"]
 ["T10191", "war; Candidatus Woesearchaeota archaeon NC_groundwater_85_Ag_S-0.1um_31_13"]
 ["T04015", "loki; Candidatus Lokiarchaeum sp. GC14_75"]
 ["T09593", "lob; Candidatus Lokiarchaeum ossiferum"]
 ["T06555", "psyt; Promethearchaeum syntrophicum"]
 ["T09928", "oyw; Candidatus Odinarchaeum yellowstonii"]
 ["T03835", "agw; Archaeon GW2011_AR10"]
 ["T03843", "arg; Archaeon GW2011_AR20"]

Error handling

KEGGAPI lets HTTP.jl exceptions propagate. An unsuccessful HTTP response throws HTTP.Exceptions.StatusError. Connection, request, and timeout failures throw HTTP.Exceptions.ConnectError, HTTP.Exceptions.RequestError, and HTTP.Exceptions.TimeoutError, respectively. See KEGGAPI.request for the low-level request contract.

See Examples for more calls and API reference for the full interface.