Update GeneFinder module and add tests

Manifest.toml

@@ -1,12 +1,8 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.9.4"
+julia_version = "1.10.0"
 manifest_format = "2.0"
-project_hash = "51fd5132cd6ba02b6fa80c05982319be6520bdf4"
-
-[[deps.ArgTools]]
-uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
-version = "1.1.1"
+project_hash = "adaf35fb55ecd7280ba5cc9b0adc89489f2fd31c"
 
 [[deps.Artifacts]]
 uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
@@ -27,10 +23,10 @@ uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
 version = "0.1.4"
 
 [[deps.BioMarkovChains]]
-deps = ["BioSequences", "PrecompileTools", "StatsAPI", "TestItemRunner", "TestItems", "VectorizedKmers"]
-git-tree-sha1 = "8ba82351d84233c9d140df8df21dfe3fb535a251"
+deps = ["BioSequences", "PrecompileTools", "VectorizedKmers"]
+git-tree-sha1 = "44da2d71c2e9a68babb324c4df69d87b9ff7a835"
 uuid = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
-version = "0.8.0"
+version = "0.9.0"
 
     [deps.BioMarkovChains.extensions]
     DiscreteMarkovChainsExt = "DiscreteMarkovChains"
@@ -54,9 +50,9 @@ version = "5.1.3"
 
 [[deps.Compat]]
 deps = ["UUIDs"]
-git-tree-sha1 = "8a62af3e248a8c4bad6b32cbbe663ae02275e32c"
+git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
-version = "4.10.0"
+version = "4.10.1"
 weakdeps = ["Dates", "LinearAlgebra"]
 
     [deps.Compat.extensions]
@@ -65,7 +61,7 @@ weakdeps = ["Dates", "LinearAlgebra"]
 [[deps.CompilerSupportLibraries_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
-version = "1.0.5+0"
+version = "1.0.5+1"
 
 [[deps.DataAPI]]
 git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c"
@@ -88,11 +84,6 @@ git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
 uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
-[[deps.Downloads]]
-deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
-uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
-version = "1.6.0"
-
 [[deps.FASTX]]
 deps = ["Automa", "BioGenerics", "PrecompileTools", "StringViews", "TranscodingStreams"]
 git-tree-sha1 = "bff5d62bf5e1c382a370ac701bcaea9a24115ac6"
@@ -103,9 +94,6 @@ weakdeps = ["BioSequences"]
     [deps.FASTX.extensions]
     BioSequencesExt = "BioSequences"
 
-[[deps.FileWatching]]
-uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
-
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
@@ -116,24 +104,19 @@ uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
 version = "0.2.2"
 
 [[deps.IterTools]]
-git-tree-sha1 = "4ced6667f9974fc5c5943fa5e2ef1ca43ea9e450"
+git-tree-sha1 = "274c38bd733f9d29036d0a73658fff1dc1d3a065"
 uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
-version = "1.8.0"
-
-[[deps.LibCURL]]
-deps = ["LibCURL_jll", "MozillaCACerts_jll"]
-uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
-version = "0.6.4"
-
-[[deps.LibCURL_jll]]
-deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll", "Zlib_jll", "nghttp2_jll"]
-uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
-version = "8.4.0+0"
+version = "1.9.0"
 
 [[deps.LibGit2]]
-deps = ["Base64", "NetworkOptions", "Printf", "SHA"]
+deps = ["Base64", "LibGit2_jll", "NetworkOptions", "Printf", "SHA"]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
 
+[[deps.LibGit2_jll]]
+deps = ["Artifacts", "LibSSH2_jll", "Libdl", "MbedTLS_jll"]
+uuid = "e37daf67-58a4-590a-8e99-b0245dd2ffc5"
+version = "1.6.4+0"
+
 [[deps.LibSSH2_jll]]
 deps = ["Artifacts", "Libdl", "MbedTLS_jll"]
 uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
@@ -162,46 +145,34 @@ version = "0.3.26"
     ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
     InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"
 
-[[deps.Logging]]
-uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
-
 [[deps.Markdown]]
 deps = ["Base64"]
 uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
 
 [[deps.MbedTLS_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
-version = "2.28.2+0"
+version = "2.28.2+1"
 
 [[deps.Missings]]
 deps = ["DataAPI"]
 git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272"
 uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
 version = "1.1.0"
 
-[[deps.MozillaCACerts_jll]]
-uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
-version = "2022.10.11"
-
 [[deps.NetworkOptions]]
 uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
 version = "1.2.0"
 
 [[deps.OpenBLAS_jll]]
 deps = ["Artifacts", "CompilerSupportLibraries_jll", "Libdl"]
 uuid = "4536629a-c528-5b80-bd46-f80d51c5b363"
-version = "0.3.21+4"
+version = "0.3.23+2"
 
 [[deps.OrderedCollections]]
-git-tree-sha1 = "2e73fe17cac3c62ad1aebe70d44c963c3cfdc3e3"
+git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
-version = "1.6.2"
-
-[[deps.Pkg]]
-deps = ["Artifacts", "Dates", "Downloads", "FileWatching", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "Serialization", "TOML", "Tar", "UUIDs", "p7zip_jll"]
-uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
-version = "1.9.2"
+version = "1.6.3"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
@@ -219,12 +190,8 @@ version = "1.4.1"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[deps.REPL]]
-deps = ["InteractiveUtils", "Markdown", "Sockets", "Unicode"]
-uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
-
 [[deps.Random]]
-deps = ["SHA", "Serialization"]
+deps = ["SHA"]
 uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 
 [[deps.SHA]]
@@ -234,23 +201,21 @@ version = "0.7.0"
 [[deps.Serialization]]
 uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
 
-[[deps.Sockets]]
-uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
-
 [[deps.SortingAlgorithms]]
 deps = ["DataStructures"]
-git-tree-sha1 = "5165dfb9fd131cf0c6957a3a7605dede376e7b63"
+git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085"
 uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
-version = "1.2.0"
+version = "1.2.1"
 
 [[deps.SparseArrays]]
 deps = ["Libdl", "LinearAlgebra", "Random", "Serialization", "SuiteSparse_jll"]
 uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
+version = "1.10.0"
 
 [[deps.Statistics]]
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
-version = "1.9.0"
+version = "1.10.0"
 
 [[deps.StatsAPI]]
 deps = ["LinearAlgebra"]
@@ -270,44 +235,27 @@ uuid = "354b36f9-a18e-4713-926e-db85100087ba"
 version = "1.3.3"
 
 [[deps.SuiteSparse_jll]]
-deps = ["Artifacts", "Libdl", "Pkg", "libblastrampoline_jll"]
+deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
 uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
-version = "5.10.1+6"
+version = "7.2.1+1"
 
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 version = "1.0.3"
 
-[[deps.Tar]]
-deps = ["ArgTools", "SHA"]
-uuid = "a4e569a6-e804-4fa4-b0f3-eef7a1d5b13e"
-version = "1.10.0"
-
-[[deps.Test]]
-deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
-uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-
-[[deps.TestItemRunner]]
-deps = ["Pkg", "TOML", "Test", "TestItems", "UUIDs"]
-git-tree-sha1 = "7351f1f7389e048ce974b2c176513b817c94b15f"
-uuid = "f8b46487-2199-4994-9208-9a1283c18c0a"
-version = "0.2.2"
-
-[[deps.TestItems]]
-git-tree-sha1 = "8621ba2637b49748e2dc43ba3d84340be2938022"
-uuid = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
-version = "0.1.1"
-
 [[deps.TranscodingStreams]]
 git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
 version = "0.10.2"
-weakdeps = ["Random", "Test"]
 
     [deps.TranscodingStreams.extensions]
     TestExt = ["Test", "Random"]
 
+    [deps.TranscodingStreams.weakdeps]
+    Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
+    Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+
 [[deps.Twiddle]]
 git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
 uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
@@ -321,35 +269,15 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[deps.VectorizedKmers]]
-git-tree-sha1 = "efb4ffc102a47fce6d9ad94c7689a7c65b408db8"
+git-tree-sha1 = "eaf497f1b720ae17dc52463dfe5fed5f74b0e4df"
 uuid = "2ef45bd6-4c2b-43d8-88b3-40597287359a"
-version = "0.7.0"
+version = "0.8.1"
+weakdeps = ["BioSequences"]
 
     [deps.VectorizedKmers.extensions]
-    BioSeqCUDAExt = ["BioSequences", "CUDA"]
     BioSequencesExt = "BioSequences"
-    CUDAExt = "CUDA"
-
-    [deps.VectorizedKmers.weakdeps]
-    BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-    CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
-
-[[deps.Zlib_jll]]
-deps = ["Libdl"]
-uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
-version = "1.2.13+0"
 
 [[deps.libblastrampoline_jll]]
 deps = ["Artifacts", "Libdl"]
 uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
-version = "5.8.0+0"
-
-[[deps.nghttp2_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
-version = "1.52.0+1"
-
-[[deps.p7zip_jll]]
-deps = ["Artifacts", "Libdl"]
-uuid = "3f19e933-33d8-53b3-aaab-bd5110c3b7a0"
-version = "17.4.0+0"
+version = "5.8.0+1"

Project.toml

@@ -1,6 +1,6 @@
 name = "GeneFinder"
 uuid = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
-authors = ["Camilo García"]
+authors = ["Camilo García-Botero"]
 version = "0.0.23"
 
 [deps]
@@ -11,22 +11,17 @@ FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
-TestItems = "1c621080-faea-4a02-84b6-bbd5e436b8fe"
 
 [compat]
-BioSequences = "^3"
-FASTX = "^2"
+BioSequences = "3"
+FASTX = "2"
 IterTools = "1.4"
 PrecompileTools = "1"
-StatsBase = "^0.34.0"
-TestItemRunner = "0.2"
-TestItems = "0.1"
-julia = "^1.6.0"
+StatsBase = "0.34.0"
+julia = "1"
 
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
-TestItemRunner = "f8b46487-2199-4994-9208-9a1283c18c0a"
 
 [targets]
 test = ["Test"]

src/GeneFinder.jl

@@ -1,6 +1,5 @@
 module GeneFinder
 
-using Automa: RegExp
 using BioSequences:
     DNA,
     DNA_Gap, DNA_A, DNA_C, DNA_M, DNA_G, DNA_R, DNA_S, DNA_V, DNA_T, DNA_W, DNA_Y, DNA_H, DNA_K, DNA_D, DNA_B, DNA_N,
@@ -15,14 +14,15 @@ using BioSequences:
     @biore_str,
     @dna_str,
     GeneticCode,
-    reverse_complement
+    reverse_complement,
+    randdnaseq
+
 
 using BioMarkovChains: BioMarkovChain
 using FASTX: FASTA, sequence, FASTAReader
 using IterTools: takewhile, iterated
 using PrecompileTools: @setup_workload, @compile_workload
 using StatsBase: countmap
-using TestItems: @testitem
 
 include("types.jl")
 export ORF
@@ -41,14 +41,13 @@ include("extended.jl")
 @setup_workload begin
     # Putting some things in `@setup_workload` instead of `@compile_workload` can reduce the size of the
     # precompile file and potentially make loading faster.
-    using BioSequences
     seq = randdnaseq(99)
     @compile_workload begin
         # all calls in this block will be precompiled, regardless of whether
         # they belong to your package or not (on Julia 1.8 and higher)
         findorfs(seq)
         getorfdna(seq)
-        getorfaa(seq)
+        # getorfaa(seq)
     end
 end