Merge pull request #28 from camilogarciabotero/newalgorithm

Add a new ORF finder method algorithm using BioMarkovChains.jl

Manifest.toml

@@ -2,7 +2,33 @@
 
 julia_version = "1.10.2"
 manifest_format = "2.0"
-project_hash = "0426921543f1f35e1faa99ad2688f4a61508977b"
+project_hash = "b881dd48d80d6b19dfa1756a0b2d6e2e42d93e33"
+
+[[deps.Automa]]
+deps = ["PrecompileTools", "TranscodingStreams"]
+git-tree-sha1 = "588e0d680ad1d7201d4c6a804dcb1cd9cba79fbb"
+uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
+version = "1.0.3"
+
+[[deps.BioGenerics]]
+deps = ["TranscodingStreams"]
+git-tree-sha1 = "7bbc085aebc6faa615740b63756e4986c9e85a70"
+uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
+version = "0.1.4"
+
+[[deps.BioMarkovChains]]
+deps = ["BioSequences", "PrecompileTools", "VectorizedKmers"]
+git-tree-sha1 = "c48cc4efe18355a1a19ae627d05bf19df0a57253"
+uuid = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
+version = "0.9.3"
+
+    [deps.BioMarkovChains.extensions]
+    DiscreteMarkovChainsExt = "DiscreteMarkovChains"
+    MarkovChainHammerExt = "MarkovChainHammer"
+
+    [deps.BioMarkovChains.weakdeps]
+    DiscreteMarkovChains = "8abcb7ef-b365-4f7b-ac38-56893fb62f9f"
+    MarkovChainHammer = "38c40fd0-bccb-4723-b30d-b2caea0ad8d9"
 
 [[deps.BioSequences]]
 deps = ["BioSymbols", "PrecompileTools", "Random", "Twiddle"]
@@ -20,6 +46,16 @@ version = "5.1.3"
 deps = ["Printf"]
 uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
 
+[[deps.FASTX]]
+deps = ["Automa", "BioGenerics", "PrecompileTools", "StringViews", "TranscodingStreams"]
+git-tree-sha1 = "bff5d62bf5e1c382a370ac701bcaea9a24115ac6"
+uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
+version = "2.1.4"
+weakdeps = ["BioSequences"]
+
+    [deps.FASTX.extensions]
+    BioSequencesExt = "BioSequences"
+
 [[deps.IterTools]]
 git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023"
 uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
@@ -49,15 +85,47 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 version = "0.7.0"
 
+[[deps.StaticArraysCore]]
+git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d"
+uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
+version = "1.4.2"
+
+[[deps.StringViews]]
+git-tree-sha1 = "f7b06677eae2571c888fd686ba88047d8738b0e3"
+uuid = "354b36f9-a18e-4713-926e-db85100087ba"
+version = "1.3.3"
+
 [[deps.TOML]]
 deps = ["Dates"]
 uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
 version = "1.0.3"
 
+[[deps.TranscodingStreams]]
+git-tree-sha1 = "71509f04d045ec714c4748c785a59045c3736349"
+uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
+version = "0.10.7"
+
+    [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"
 version = "1.1.2"
 
 [[deps.Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
+
+[[deps.VectorizedKmers]]
+deps = ["StaticArraysCore"]
+git-tree-sha1 = "c2a7ec780efdf917088b5b65f78f402f72a2eb01"
+uuid = "2ef45bd6-4c2b-43d8-88b3-40597287359a"
+version = "0.9.2"
+weakdeps = ["BioSequences"]
+
+    [deps.VectorizedKmers.extensions]
+    BioSequencesExt = "BioSequences"

Project.toml

@@ -4,12 +4,16 @@ authors = ["Camilo García-Botero"]
 version = "0.2.0"
 
 [deps]
+BioMarkovChains = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
+FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 
 [compat]
+BioMarkovChains = "0.9"
 BioSequences = "3"
+FASTX = "2"
 IterTools = "1.4"
 PrecompileTools = "1"
 julia = "1"

docs/Manifest.toml

@@ -1,6 +1,6 @@
 # This file is machine-generated - editing it directly is not advised
 
-julia_version = "1.10.0"
+julia_version = "1.10.2"
 manifest_format = "2.0"
 project_hash = "e796693959137d83427b789f5054fa800312cae0"
 
@@ -10,9 +10,9 @@ uuid = "a4c015fc-c6ff-483c-b24f-f7ea428134e9"
 version = "0.0.1"
 
 [[deps.AbstractTrees]]
-git-tree-sha1 = "faa260e4cb5aba097a73fab382dd4b5819d8ec8c"
+git-tree-sha1 = "2d9c9a55f9c93e8887ad391fbae72f8ef55e1177"
 uuid = "1520ce14-60c1-5f80-bbc7-55ef81b5835c"
-version = "0.4.4"
+version = "0.4.5"
 
 [[deps.ArgTools]]
 uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
@@ -23,9 +23,9 @@ uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
 
 [[deps.Automa]]
 deps = ["PrecompileTools", "TranscodingStreams"]
-git-tree-sha1 = "0da671c730d79b8f9a88a391556ec695ea921040"
+git-tree-sha1 = "588e0d680ad1d7201d4c6a804dcb1cd9cba79fbb"
 uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
-version = "1.0.2"
+version = "1.0.3"
 
 [[deps.Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
@@ -38,9 +38,9 @@ version = "0.1.4"
 
 [[deps.BioMarkovChains]]
 deps = ["BioSequences", "PrecompileTools", "VectorizedKmers"]
-git-tree-sha1 = "44da2d71c2e9a68babb324c4df69d87b9ff7a835"
+git-tree-sha1 = "c48cc4efe18355a1a19ae627d05bf19df0a57253"
 uuid = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
-version = "0.9.0"
+version = "0.9.3"
 
     [deps.BioMarkovChains.extensions]
     DiscreteMarkovChainsExt = "DiscreteMarkovChains"
@@ -69,15 +69,15 @@ version = "0.1.8"
 
 [[deps.CodecZlib]]
 deps = ["TranscodingStreams", "Zlib_jll"]
-git-tree-sha1 = "cd67fc487743b2f0fd4380d4cbd3a24660d0eec8"
+git-tree-sha1 = "59939d8a997469ee05c4b4944560a820f9ba0d73"
 uuid = "944b1d66-785c-5afd-91f1-9de20f533193"
-version = "0.7.3"
+version = "0.7.4"
 
 [[deps.ConcurrentUtilities]]
 deps = ["Serialization", "Sockets"]
-git-tree-sha1 = "8cfa272e8bdedfa88b6aefbbca7c19f1befac519"
+git-tree-sha1 = "6cbbd4d241d7e6579ab354737f4dd95ca43946e1"
 uuid = "f0e56b4a-5159-44fe-b623-3e5288b988bb"
-version = "2.3.0"
+version = "2.4.1"
 
 [[deps.Dates]]
 deps = ["Printf"]
@@ -90,10 +90,10 @@ uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
 version = "0.9.3"
 
 [[deps.Documenter]]
-deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "Test", "Unicode"]
-git-tree-sha1 = "2613dbec8f4748273bbe30ba71fd5cb369966bac"
+deps = ["ANSIColoredPrinters", "AbstractTrees", "Base64", "CodecZlib", "Dates", "DocStringExtensions", "Downloads", "Git", "IOCapture", "InteractiveUtils", "JSON", "LibGit2", "Logging", "Markdown", "MarkdownAST", "Pkg", "PrecompileTools", "REPL", "RegistryInstances", "SHA", "TOML", "Test", "Unicode"]
+git-tree-sha1 = "4a40af50e8b24333b9ec6892546d9ca5724228eb"
 uuid = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
-version = "1.2.1"
+version = "1.3.0"
 
 [[deps.Downloads]]
 deps = ["ArgTools", "FileWatching", "LibCURL", "NetworkOptions"]
@@ -126,34 +126,34 @@ weakdeps = ["BioSequences"]
 uuid = "7b1f6079-737a-58dc-b8bc-7a2ca5c1b5ee"
 
 [[deps.GeneFinder]]
-deps = ["BioSequences", "FASTX", "IterTools", "PrecompileTools"]
+deps = ["BioMarkovChains", "BioSequences", "FASTX", "IterTools", "PrecompileTools"]
 path = ".."
 uuid = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
-version = "0.1.0"
+version = "0.2.0"
 
 [[deps.Git]]
 deps = ["Git_jll"]
-git-tree-sha1 = "51764e6c2e84c37055e846c516e9015b4a291c7d"
+git-tree-sha1 = "04eff47b1354d702c3a85e8ab23d539bb7d5957e"
 uuid = "d7ba0133-e1db-5d97-8f8c-041e4b3a1eb2"
-version = "1.3.0"
+version = "1.3.1"
 
 [[deps.Git_jll]]
 deps = ["Artifacts", "Expat_jll", "JLLWrappers", "LibCURL_jll", "Libdl", "Libiconv_jll", "OpenSSL_jll", "PCRE2_jll", "Zlib_jll"]
-git-tree-sha1 = "bb8f7cc77ec1152414b2af6db533d9471cfbb2d1"
+git-tree-sha1 = "12945451c5d0e2d0dca0724c3a8d6448b46bbdf9"
 uuid = "f8c6e375-362e-5223-8a59-34ff63f689eb"
-version = "2.42.0+0"
+version = "2.44.0+1"
 
 [[deps.HTTP]]
 deps = ["Base64", "CodecZlib", "ConcurrentUtilities", "Dates", "ExceptionUnwrapping", "Logging", "LoggingExtras", "MbedTLS", "NetworkOptions", "OpenSSL", "Random", "SimpleBufferStream", "Sockets", "URIs", "UUIDs"]
-git-tree-sha1 = "abbbb9ec3afd783a7cbd82ef01dcd088ea051398"
+git-tree-sha1 = "8e59b47b9dc525b70550ca082ce85bcd7f5477cd"
 uuid = "cd3eb016-35fb-5094-929b-558a96fad6f3"
-version = "1.10.1"
+version = "1.10.5"
 
 [[deps.IOCapture]]
 deps = ["Logging", "Random"]
-git-tree-sha1 = "d75853a0bdbfb1ac815478bacd89cd27b550ace6"
+git-tree-sha1 = "8b72179abc660bfab5e28472e019392b97d0985c"
 uuid = "b5f81e59-6552-4d32-b1f0-c071b021bf89"
-version = "0.2.3"
+version = "0.2.4"
 
 [[deps.InteractiveUtils]]
 deps = ["Markdown"]
@@ -268,15 +268,15 @@ version = "1.2.0"
 
 [[deps.OpenSSL]]
 deps = ["BitFlags", "Dates", "MozillaCACerts_jll", "OpenSSL_jll", "Sockets"]
-git-tree-sha1 = "51901a49222b09e3743c65b8847687ae5fc78eb2"
+git-tree-sha1 = "af81a32750ebc831ee28bdaaba6e1067decef51e"
 uuid = "4d8831e6-92b7-49fb-bdf8-b643e874388c"
-version = "1.4.1"
+version = "1.4.2"
 
 [[deps.OpenSSL_jll]]
 deps = ["Artifacts", "JLLWrappers", "Libdl"]
-git-tree-sha1 = "cc6e1927ac521b659af340e0ca45828a3ffc748f"
+git-tree-sha1 = "60e3045590bd104a16fefb12836c00c0ef8c7f8c"
 uuid = "458c3c95-2e84-50aa-8efc-19380b2a3a95"
-version = "3.0.12+0"
+version = "3.0.13+0"
 
 [[deps.PCRE2_jll]]
 deps = ["Artifacts", "Libdl"]
@@ -296,15 +296,15 @@ version = "1.10.0"
 
 [[deps.PrecompileTools]]
 deps = ["Preferences"]
-git-tree-sha1 = "03b4c25b43cb84cee5c90aa9b5ea0a78fd848d2f"
+git-tree-sha1 = "5aa36f7049a63a1528fe8f7c3f2113413ffd4e1f"
 uuid = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
-version = "1.2.0"
+version = "1.2.1"
 
 [[deps.Preferences]]
 deps = ["TOML"]
-git-tree-sha1 = "00805cd429dcb4870060ff49ef443486c262e38e"
+git-tree-sha1 = "9306f6085165d270f7e3db02af26a400d580f5c6"
 uuid = "21216c6a-2e73-6563-6e65-726566657250"
-version = "1.4.1"
+version = "1.4.3"
 
 [[deps.Printf]]
 deps = ["Unicode"]
@@ -339,6 +339,11 @@ version = "1.1.0"
 [[deps.Sockets]]
 uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
 
+[[deps.StaticArraysCore]]
+git-tree-sha1 = "36b3d696ce6366023a0ea192b4cd442268995a0d"
+uuid = "1e83bf80-4336-4d27-bf5d-d5a4f845583c"
+version = "1.4.2"
+
 [[deps.StringViews]]
 git-tree-sha1 = "f7b06677eae2571c888fd686ba88047d8738b0e3"
 uuid = "354b36f9-a18e-4713-926e-db85100087ba"
@@ -359,9 +364,9 @@ deps = ["InteractiveUtils", "Logging", "Random", "Serialization"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[deps.TranscodingStreams]]
-git-tree-sha1 = "1fbeaaca45801b4ba17c251dd8603ef24801dd84"
+git-tree-sha1 = "71509f04d045ec714c4748c785a59045c3736349"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.10.2"
+version = "0.10.7"
 weakdeps = ["Random", "Test"]
 
     [deps.TranscodingStreams.extensions]
@@ -385,9 +390,10 @@ uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
 
 [[deps.VectorizedKmers]]
-git-tree-sha1 = "eaf497f1b720ae17dc52463dfe5fed5f74b0e4df"
+deps = ["StaticArraysCore"]
+git-tree-sha1 = "c2a7ec780efdf917088b5b65f78f402f72a2eb01"
 uuid = "2ef45bd6-4c2b-43d8-88b3-40597287359a"
-version = "0.8.1"
+version = "0.9.2"
 weakdeps = ["BioSequences"]
 
     [deps.VectorizedKmers.extensions]

docs/make.jl

@@ -5,7 +5,7 @@ DocMeta.setdocmeta!(GeneFinder, :DocTestSetup, :(using GeneFinder); recursive =
 
 makedocs(;
     modules = [GeneFinder],
-    authors = "Camilo García",
+    authors = "Camilo García-Botero",
     repo = "https://github.com/camilogarciabotero/GeneFinder.jl/",
     sitename = "GeneFinder.jl",
     format = Documenter.HTML(;
@@ -17,15 +17,13 @@ makedocs(;
     ),
     pages = [
         "Home" => "index.md",
-        "Finding ORFs" => "simplefinder.md",
-        "Wrtiting ORFs in files" => "iodocs.md",
-        # "A Simple coding rule" => "simplecodingrule.md",
-        "Roadmap" => "roadmap.md",
+        "Finding ORFs" => "naivefinder.md",
+        "A Simple Coding Rule" => "simplecodingrule.md",
+        "Wrtiting ORFs In Files" => "iodocs.md",
         "API" => "api.md",
+        # "Roadmap" => "roadmap.md",
     ],
+    warnonly = true,
 )
 
-deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")
-
-
-# blob/{commit}{path}#{line}
+deploydocs(; repo = "https://github.com/camilogarciabotero/GeneFinder.jl", devbranch = "main")