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Enhance UniProt ID handling #36

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Merged
timholy merged 1 commit into from
Apr 30, 2025
Merged

Enhance UniProt ID handling #36

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23 changes: 13 additions & 10 deletions src/naming_conventions.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -64,6 +64,9 @@ julia> uniprotX("Q8VGW6_MOUSE/31-308")
```
"""
function uniprotX(name::AbstractString)::AbstractString
if startswith(name, "tr|") || startswith(name, "sp|")
name = name[4:end]
end
m = match(rex_uniprotX_Swiss, name)
m !== nothing && return m.captures[1]
m = match(rex_uniprot_accession, name)
Expand Down Expand Up @@ -101,7 +104,7 @@ function query_uniprot_accession(id)
end

"""
jobID = GPCRAnalysis.map_uniprot_submit(ids, from, to="UniProtKB")
jobID = GPCRAnalysis.map_uniprot_submit(ids, from="UniProtKB_AC-ID", to="UniProtKB")

Submit a list of `ids` to the Uniprot ID mapping service, to convert from ID convention `from` to `to`.
The jobID can be used to check the status (`map_uniprot_status`) and retrieve the results (`map_uniprot_retrieve`).
Expand All @@ -111,24 +114,24 @@ The jobID can be used to check the status (`map_uniprot_status`) and retrieve th
julia> jobID = GPCRAnalysis.map_uniprot_submit(["ENSMUSG00000067064", "ENSMUSG00000057464"], "Ensembl");
```
"""
function map_uniprot_submit(ids::AbstractString, from::AbstractString, to::AbstractString="UniProtKB")
function map_uniprot_submit(ids::AbstractString, from::AbstractString="UniProtKB_AC-ID", to::AbstractString="UniProtKB")
resp = HTTP.post("https://rest.uniprot.org/idmapping/run", [],
Dict("from" => from, "to" => "UniProtKB", "ids" => ids))
Dict("from" => from, "to" => to, "ids" => ids))
if resp.status == 200
return JSON3.read(String(resp.body))["jobId"]
end
return nothing
end
map_uniprot_submit(ids::AbstractVector, from::AbstractString) = map_uniprot_submit(join(ids, ','), from)
map_uniprot_submit(ids::AbstractVector, args...) = map_uniprot_submit(join(ids, ','), args...)

"""
status = GPCRAnalysis.map_uniprot_status(jobId)
status = GPCRAnalysis.map_uniprot_status(jobID)

Check the status of a Uniprot ID mapping job. Returns `true` if the results are
ready. Otherwise, returns the status object.
"""
function map_uniprot_status(jobId)
resp = HTTP.get("https://rest.uniprot.org/idmapping/status/$jobId", ["Accept" => "application/json"])
function map_uniprot_status(jobID)
resp = HTTP.get("https://rest.uniprot.org/idmapping/status/$jobID", ["Accept" => "application/json"]; decompress = true)
if resp.status == 200
status = JSON3.read(String(HTTP.decode(resp)))
haskey(status, "results") && return true
Expand All @@ -138,12 +141,12 @@ function map_uniprot_status(jobId)
end

"""
result = GPCRAnalysis.map_uniprot_retrieve(jobId)
result = GPCRAnalysis.map_uniprot_retrieve(jobID)

Retrieve the results of a Uniprot ID mapping job.
"""
function map_uniprot_retrieve(jobId)
resp = HTTP.get("https://rest.uniprot.org/idmapping/stream/$jobId", ["Accept" => "application/json"])
function map_uniprot_retrieve(jobID)
resp = HTTP.get("https://rest.uniprot.org/idmapping/stream/$jobID", ["Accept" => "application/json"]; decompress = true)
if resp.status == 200
return JSON3.read(String(HTTP.decode(resp)))
end
Expand Down
16 changes: 16 additions & 0 deletions test/runtests.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -30,6 +30,8 @@ using Test
@test_throws ErrorException uniprotX("Q8VGW67_MOUSE/31-308")
@test_throws ErrorException uniprotX("q8vgw6_MOUSE/31-308")
@test_throws ErrorException uniprotX("QV8GW6_MOUSE/31-308")
# FASTA
@test @inferred(uniprotX("tr|M3WEA8|M3WEA8_FELCA Olfactory receptor family 51 subfamily S member 1 OS=Felis catus OX=9685 GN=OR51S1 PE=4 SV=2")) == "M3WEA8"

# Versioned
@test uniprotX("Q8VGW6.37") == "Q8VGW6"
Expand Down Expand Up @@ -299,6 +301,18 @@ using Test
@testset "Uniprot" begin
@test query_uniprot_accession("T2R38_MOUSE") == "Q7TQA6"

jobID = GPCRAnalysis.map_uniprot_submit(["T2R38_MOUSE"])
tstart = time()
sleep(1)
status = false
while status != true && time() < tstart + 20
sleep(1)
status = GPCRAnalysis.map_uniprot_status(jobID)
end
results = GPCRAnalysis.map_uniprot_retrieve(jobID)[:results]
resultsdict = Dict(obj["from"] => obj["to"] for obj in results)
@test resultsdict["T2R38_MOUSE"] == "Q7TQA6"

jobID = GPCRAnalysis.map_uniprot_submit(["ENSMUSG00000067064", "ENSMUSG00000057464"], "Ensembl")
tstart = time()
sleep(1)
Expand All @@ -310,6 +324,8 @@ using Test
results = GPCRAnalysis.map_uniprot_retrieve(jobID)[:results]
resultsdict = Dict(obj["from"] => obj["to"] for obj in results)
@test resultsdict["ENSMUSG00000067064"] == "Q8VGU4"


end

@testset "EBI and NCBI" begin
Expand Down
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