Rename guess_parse to bioseq

CHANGELOG.md

@@ -5,7 +5,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
 ## [3.2.0]
-* Add functions `guess_parse` and `guess_alphabet` to easily construct a biosequence
+* Add functions `bioseq` and `guess_alphabet` to easily construct a biosequence
   of an unknown alphabet from e.g. a string.
 * Relax requirement of `decode`, such that it no longer needs to check for
   invalid data. Note that this change is not breaking, since it is not possible

docs/src/construction.md

@@ -303,11 +303,11 @@ the bodies of things like for loops. And if you use them and are unsure, use the
 ```
 
 ## Loose parsing
-As of version 3.2.0, BioSequences.jl provide the [`guess_parse`](@ref) function, which can be used to build a `LongSequence`
+As of version 3.2.0, BioSequences.jl provide the [`guess`](@ref) function, which can be used to build a `LongSequence`
 from a string (or an `AbstractVector{UInt8}`) without knowing the correct `Alphabet`.
 
 ```jldoctest
-julia> guess_parse("ATGTGCTGA")
+julia> guess("ATGTGCTGA")
 9nt DNA Sequence:
 ATGTGCTGA
 ```
@@ -316,7 +316,7 @@ The function will prioritise 2-bit alphabets over 4-bit alphabets, and prefer sm
 If the input cannot be encoded by any of the built-in alphabets, an error is thrown:
 
 ```jldoctest
-julia> guess_parse("0!(CC!;#&&%")
+julia> bioseq("0!(CC!;#&&%")
 ERROR: cannot encode 0x30 in AminoAcidAlphabet
 [...]
 ```
@@ -325,7 +325,7 @@ Note that this function is only intended to be used for interactive, ephemeral w
 The function is necessarily type unstable, and the precise returned alphabet for a given input is a heuristic which is subject to change.
 
 ```@docs
-guess_parse
+bioseq
 guess_alphabet
 ```
 

src/BioSequences.jl

@@ -96,7 +96,7 @@ export
     ###
 
     guess_alphabet,
-    guess_parse,
+    bioseq,
 
     # Types & aliases
     Alphabet,

src/alphabet.jl

@@ -322,7 +322,7 @@ pick the first from the order below (i.e. `DNAAlphabet{2}()` if possible, otherw
 5. `AminoAcidAlphabet()`
 
 !!! warning
-    The functions `guess_parse` and `guess_alphabet` are intended for use in interactive
+    The functions `bioseq` and `guess_alphabet` are intended for use in interactive
     sessions, and are not suitable for use in packages or non-ephemeral work.
     They are type unstable, and their heuristics **are subject to change** in minor versions.
 

src/longsequences/constructors.jl

@@ -88,35 +88,35 @@ end
 Base.parse(::Type{LongSequence{A}}, seq::AbstractString) where A = LongSequence{A}(seq)
 
 """
-    guess_parse(s::Union{AbstractString, AbstractVector{UInt8}}) -> LongSequence
+    bioseq(s::Union{AbstractString, AbstractVector{UInt8}}) -> LongSequence
 
 Parse `s` into a `LongSequence` with an appropriate `Alphabet`, or throw an exception
 if no alphabet matches.
 See [`guess_alphabet`](@ref) for the available alphabets and the alphabet priority.
 
 !!! warning
-    The functions `guess_parse` and `guess_alphabet` are intended for use in interactive
+    The functions `bioseq` and `guess_alphabet` are intended for use in interactive
     sessions, and are not suitable for use in packages or non-ephemeral work.
     They are type unstable, and their heuristics **are subject to change** in minor versions.
 
 # Examples
 ```jldoctest
-julia> guess_parse("QMKLPEEFW")
+julia> bioseq("QMKLPEEFW")
 9aa Amino Acid Sequence:
 QMKLPEEFW
 
-julia> guess_parse("UAUGCUGUAGG")
+julia> bioseq("UAUGCUGUAGG")
 11nt RNA Sequence:
 UAUGCUGUAGG
 
-julia> guess_parse("PKMW#3>>0;kL")
+julia> bioseq("PKMW#3>>0;kL")
 ERROR: cannot encode 0x23 in AminoAcidAlphabet
 [...]
 ```
 """
-function guess_parse(s::AbstractVector{UInt8})
+function bioseq(s::AbstractVector{UInt8})
     A = guess_alphabet(s)
     A isa Integer && throw(EncodeError(AminoAcidAlphabet(), s[A]))
     LongSequence{typeof(A)}(s)
 end
-guess_parse(s::AbstractString) = guess_parse(codeunits(s))
+bioseq(s::AbstractString) = bioseq(codeunits(s))

test/alphabet.jl

@@ -198,7 +198,7 @@ end
         for S in Ss
             for T in [String, SubString, Vector{UInt8}, Test.GenericString]
                 @test guess_alphabet(T(S)) == A
-                @test guess_parse(T(S)) isa LongSequence{typeof(A)}
+                @test bioseq(T(S)) isa LongSequence{typeof(A)}
             end
         end
     end
@@ -209,7 +209,7 @@ end
     ]
         for T in [String, SubString, Vector{UInt8}, Test.GenericString]
             @test guess_alphabet(T(S)) == index
-            @test_throws BioSequences.EncodeError guess_parse(T(S))
+            @test_throws BioSequences.EncodeError bioseq(T(S))
         end
     end
 end