Merge pull request #28 from EcoJulia/feature-nearest

Improve synonyms functions

Project.toml

@@ -1,7 +1,7 @@
 name = "NCBITaxonomy"
 uuid = "f88b31d2-eb98-4433-b52d-2dd32bc6efce"
 authors = ["Timothée Poisot <[email protected]>"]
-version = "0.0.6"
+version = "0.0.7"
 
 [deps]
 Arrow = "69666777-d1a9-59fb-9406-91d4454c9d45"

docs/src/namefinding.md

@@ -5,6 +5,7 @@
 ```@docs
 taxid
 vernacular
+synonyms
 ```
 
 The `taxid` function will return a `NCBITaxon` object, which has two fields:

src/NCBITaxonomy.jl

@@ -43,7 +43,7 @@ export children, descendants
 include("lineage.jl")
 export lineage, parent, rank
 
-include("vernacular.jl")
-export vernacular
+include("nametools.jl")
+export vernacular, synonyms
 
 end

src/vernacular.jl → src/nametools.jl

@@ -12,4 +12,17 @@ function vernacular(t::NCBITaxon)
     all_names = vcat(common_names.name, genbank_names.name)
     length(all_names) == 0 && return nothing
     return unique(all_names)
+end
+
+"""
+    synonyms(t::NCBITaxon)
+
+This function will return `nothing` if no synonyms exist, and an array of names
+if they do. It returns all of the 
+"""
+function synonyms(t::NCBITaxon)
+    names_from_tax = filter(r -> r.tax_id == t.id, NCBITaxonomy.names_table)
+    syn = filter(r -> r.class == NCBITaxonomy.class_synonym, names_from_tax)
+    size(syn,1) == 0 && return nothing
+    return unique(syn.name)
 end

test/taxid.jl

@@ -46,4 +46,8 @@ module TestTaxid
     # Vernacular missing
     @test isnothing(vernacular(ncbi"Lamellodiscus elegans"))
 
+    # Synonyms
+    @test "Bos bovis" in synonyms(ncbi"Bos taurus")
+    @test isnothing(synonyms(ncbi"Lamellodiscus elegans"))
+
 end