Merge pull request #65 from banhbio/dev

Dev

Author: banhbio

src/lineage.jl

@@ -281,6 +281,26 @@ This function is useful for converting `Lineage` to `DataFrame`, for example.
 # Arguments
 
 * `fill_by_missing::Bool = false` - If `true`, fills missing instead of `UnclassifiedTaxon`.
+
+# Examples
+
+```jldoctest
+julia> ranks = [:domain, :phylum, :class, :order, :family, :genus, :species];
+
+julia> lineage = reformat(Lineage(Taxon(9606)), ranks);
+
+julia> nt = namedtuple(lineage);
+
+julia> nt.species
+9606 [species] Homo sapiens
+
+julia> incomplete = reformat(Lineage(Taxon(9443)), ranks);
+
+julia> nt = namedtuple(incomplete; fill_by_missing=true);
+
+julia> ismissing(nt.species)
+true
+```
 """
 function namedtuple(l::Lineage; fill_by_missing::Bool=false)
     ranks = l.ranks
@@ -304,6 +324,23 @@ Print a formatted representation of the lineage to the given `IO` object.
 * `delim::AbstractString = ";"` - The delimiter between taxon fields.
 * `fill::Bool = false` - If `true`, prints `UnclassifiedTaxon`. only availavle when skip is false.
 * `skip::Bool = false` - If `true`, skip printing `UnclassifiedTaxon` and delimiter.
+
+# Examples
+
+```jldoctest
+julia> ranks = [:domain, :phylum, :class, :order, :family, :genus, :species];
+
+julia> lineage = reformat(Lineage(Taxon(9443)), ranks);
+
+julia> sprint(io -> print_lineage(io, lineage))
+"Eukaryota;Chordata;Mammalia;Primates;;;"
+
+julia> sprint(io -> print_lineage(io, lineage; skip=true))
+"Eukaryota;Chordata;Mammalia;Primates"
+
+julia> sprint(io -> print_lineage(io, lineage; fill=true))
+"Eukaryota;Chordata;Mammalia;Primates;unclassified Primates family;unclassified Primates genus;unclassified Primates species"
+```
 """
 function print_lineage(io::IO, lineage::Lineage; delim::AbstractString=";", fill::Bool=false, skip::Bool=false)
     taxa = collect(lineage)

src/rank.jl

@@ -36,6 +36,16 @@ Return `CanonicalRank(sym)` if sym is in `CanonicalRanks`. Return `UnCanonicalRa
 `CanonicalRank(sym)` can be used for `isless` comparison.
 `:domain`, `:superkingdom`, and `:realm` are treated as the same top-rank
 level.
+
+# Examples
+
+```jldoctest
+julia> Rank(:species) isa Taxonomy.CanonicalRank
+true
+
+julia> Rank(:clade) isa Taxonomy.UnCanonicalRank
+true
+```
 """
 Rank
 
@@ -71,6 +81,13 @@ Return `CanonicalRank` made from `rank(taxon)` if `rank(taxon)` is in `Canonical
 `CanonicalRank(taxon)` can be used for `isless` comparison.
 `:domain`, `:superkingdom`, and `:realm` can all be handled as canonical
 aliases for the same top-rank level.
+
+# Examples
+
+```jldoctest
+julia> Rank(Taxon(9606)) isa Taxonomy.CanonicalRank
+true
+```
 """
 Rank(taxon::AbstractTaxon) = rank(taxon) |> Rank
 
@@ -86,11 +103,13 @@ Base.show(io::IO, r::Rank) = print(io, String(rank(r)))
 """
     isless(taxon::AbstractTaxon, rank::CanonicalRank)
 
-Example
-```julia
-julia> Taxon(9606 , db) < Rank(:genus)
+# Examples
+
+```jldoctest
+julia> Taxon(9606) < Rank(:genus)
 true
 ```
+
 Return `true` if the rank of the former `Taxon` is less than the later rank.
 """
 Base.isless(x1::CanonicalRank, x2::CanonicalRank) = isless(Integer(x1), Integer(x2))