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‎.gitattributes

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# Auto detect text files and perform LF normalization
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* text=auto

‎.gitignore

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*.jl.cov
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*.jl.*.cov
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*.jl.mem
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deps/deps.jl

‎Manifest.toml

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# This file is machine-generated - editing it directly is not advised
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[[ArgTools]]
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git-tree-sha1 = "bdf73eec6a88885256f282d48eafcad25d7de494"
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uuid = "0dad84c5-d112-42e6-8d28-ef12dabb789f"
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version = "1.1.1"
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[[Artifacts]]
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deps = ["Pkg"]
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git-tree-sha1 = "c30985d8821e0cd73870b17b0ed0ce6dc44cb744"
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uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
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version = "1.3.0"
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[[Automa]]
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deps = ["DataStructures", "Printf", "Random", "Test", "TranscodingStreams"]
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git-tree-sha1 = "c81526bf5f6fb4616b4e22a3cd62ac20e255fd3c"
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uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
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version = "0.8.0"
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[[Base64]]
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uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
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[[BioGenerics]]
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deps = ["TranscodingStreams"]
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git-tree-sha1 = "57deb413ca9f4c8bc7d4c6e98ebe217ff728c737"
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uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
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version = "0.1.0"
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[[BioSequences]]
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deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "StableRNGs", "Twiddle"]
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git-tree-sha1 = "093ccb9211bdc71924abf8e74a0790af11da35a7"
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uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
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version = "2.0.5"
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[[BioSymbols]]
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deps = ["Automa"]
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git-tree-sha1 = "ec77888ac3e78f9d372c2b533bdb52668f9e2b09"
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uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
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version = "4.0.4"
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[[Combinatorics]]
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git-tree-sha1 = "08c8b6831dc00bfea825826be0bc8336fc369860"
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uuid = "861a8166-3701-5b0c-9a16-15d98fcdc6aa"
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version = "1.0.2"
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[[Compat]]
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deps = ["Base64", "Dates", "DelimitedFiles", "Distributed", "InteractiveUtils", "LibGit2", "Libdl", "LinearAlgebra", "Markdown", "Mmap", "Pkg", "Printf", "REPL", "Random", "SHA", "Serialization", "SharedArrays", "Sockets", "SparseArrays", "Statistics", "Test", "UUIDs", "Unicode"]
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git-tree-sha1 = "919c7f3151e79ff196add81d7f4e45d91bbf420b"
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uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
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version = "3.25.0"
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[[DataStructures]]
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deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
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git-tree-sha1 = "4437b64df1e0adccc3e5d1adbc3ac741095e4677"
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uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
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version = "0.18.9"
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[[Dates]]
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deps = ["Printf"]
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uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"
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[[DelimitedFiles]]
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deps = ["Mmap"]
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uuid = "8bb1440f-4735-579b-a4ab-409b98df4dab"
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[[Distributed]]
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deps = ["Random", "Serialization", "Sockets"]
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uuid = "8ba89e20-285c-5b6f-9357-94700520ee1b"
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[[Downloads]]
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deps = ["ArgTools", "LibCURL", "NetworkOptions"]
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git-tree-sha1 = "5de8c54d269fd7ab430656c27de73e63eb07a979"
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uuid = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
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version = "1.4.0"
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[[FASTX]]
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deps = ["Automa", "BioGenerics", "BioSequences", "BioSymbols", "TranscodingStreams"]
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git-tree-sha1 = "a980d6ac14c84c3ed17d0d07a0963a1c6d074b34"
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uuid = "c2308a5c-f048-11e8-3e8a-31650f418d12"
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version = "1.1.3"
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[[IndexableBitVectors]]
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deps = ["Random", "Test"]
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git-tree-sha1 = "b7f5e42dc867b8a8654a5f899064632dac05bc82"
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uuid = "1cb3b9ac-1ffd-5777-9e6b-a3d42300664d"
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version = "1.0.0"
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[[InteractiveUtils]]
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deps = ["Markdown"]
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uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
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[[JLLWrappers]]
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git-tree-sha1 = "a431f5f2ca3f4feef3bd7a5e94b8b8d4f2f647a0"
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uuid = "692b3bcd-3c85-4b1f-b108-f13ce0eb3210"
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version = "1.2.0"
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[[LibCURL]]
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deps = ["LibCURL_jll", "MozillaCACerts_jll"]
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git-tree-sha1 = "cdbe7465ab7b52358804713a53c7fe1dac3f8a3f"
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uuid = "b27032c2-a3e7-50c8-80cd-2d36dbcbfd21"
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version = "0.6.3"
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[[LibCURL_jll]]
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deps = ["LibSSH2_jll", "Libdl", "MbedTLS_jll", "Pkg", "Zlib_jll", "nghttp2_jll"]
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git-tree-sha1 = "897d962c20031e6012bba7b3dcb7a667170dad17"
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uuid = "deac9b47-8bc7-5906-a0fe-35ac56dc84c0"
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version = "7.70.0+2"
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[[LibGit2]]
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deps = ["Printf"]
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uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
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[[LibSSH2_jll]]
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deps = ["Libdl", "MbedTLS_jll", "Pkg"]
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git-tree-sha1 = "717705533148132e5466f2924b9a3657b16158e8"
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uuid = "29816b5a-b9ab-546f-933c-edad1886dfa8"
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version = "1.9.0+3"
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[[Libdl]]
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uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"
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[[LinearAlgebra]]
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deps = ["Libdl"]
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uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
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[[Logging]]
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uuid = "56ddb016-857b-54e1-b83d-db4d58db5568"
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[[Markdown]]
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deps = ["Base64"]
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uuid = "d6f4376e-aef5-505a-96c1-9c027394607a"
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[[MbedTLS_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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git-tree-sha1 = "0eef589dd1c26a3ac9d753fe1a8bcad63f956fa6"
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uuid = "c8ffd9c3-330d-5841-b78e-0817d7145fa1"
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version = "2.16.8+1"
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[[Mmap]]
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uuid = "a63ad114-7e13-5084-954f-fe012c677804"
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[[MozillaCACerts_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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git-tree-sha1 = "bbcac5afd9049834366c3b68d792971e3d981799"
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uuid = "14a3606d-f60d-562e-9121-12d972cd8159"
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version = "2020.10.14+0"
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[[NetworkOptions]]
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git-tree-sha1 = "ed3157f48a05543cce9b241e1f2815f7e843d96e"
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uuid = "ca575930-c2e3-43a9-ace4-1e988b2c1908"
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version = "1.2.0"
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[[OrderedCollections]]
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git-tree-sha1 = "4fa2ba51070ec13fcc7517db714445b4ab986bdf"
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uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
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version = "1.4.0"
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[[Pkg]]
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deps = ["Dates", "LibGit2", "Libdl", "Logging", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
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uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
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[[Printf]]
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deps = ["Unicode"]
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uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
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[[REPL]]
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deps = ["InteractiveUtils", "Markdown", "Sockets"]
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uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
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[[Random]]
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deps = ["Serialization"]
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uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
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[[SHA]]
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uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
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[[Serialization]]
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uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"
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[[SharedArrays]]
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deps = ["Distributed", "Mmap", "Random", "Serialization"]
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uuid = "1a1011a3-84de-559e-8e89-a11a2f7dc383"
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[[Sockets]]
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uuid = "6462fe0b-24de-5631-8697-dd941f90decc"
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[[SparseArrays]]
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deps = ["LinearAlgebra", "Random"]
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uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
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[[StableRNGs]]
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deps = ["Random", "Test"]
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git-tree-sha1 = "b57c4216b6c163a3a9d674f6b9f7b99cdccdb959"
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uuid = "860ef19b-820b-49d6-a774-d7a799459cd3"
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version = "0.1.2"
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[[Statistics]]
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deps = ["LinearAlgebra", "SparseArrays"]
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uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
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[[Test]]
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deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
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uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
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[[TranscodingStreams]]
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deps = ["Random", "Test"]
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git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
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uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
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version = "0.9.5"
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[[Twiddle]]
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git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
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uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
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version = "1.1.2"
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[[UUIDs]]
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deps = ["Random", "SHA"]
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uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
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[[Unicode]]
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uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
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[[Zlib_jll]]
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deps = ["Artifacts", "JLLWrappers", "Libdl", "Pkg"]
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git-tree-sha1 = "320228915c8debb12cb434c59057290f0834dbf6"
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uuid = "83775a58-1f1d-513f-b197-d71354ab007a"
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version = "1.2.11+18"
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[[nghttp2_jll]]
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deps = ["Libdl", "Pkg"]
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git-tree-sha1 = "8e2c44ab4d49ad9518f359ed8b62f83ba8beede4"
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uuid = "8e850ede-7688-5339-a07c-302acd2aaf8d"
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version = "1.40.0+2"

‎Project.toml

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[deps]
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Downloads = "f43a241f-c20a-4ad4-852c-f6b1247861c6"
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FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"

‎README.md

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# BioFetch.jl
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Easily fetch biological sequences from online sources

‎src/BioFetch.jl

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module BioFetch
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using Downloads
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using FASTX
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const ENTREZ_BASE_URL = raw"https://eutils.ncbi.nlm.nih.gov/entrez/eutils/"
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const ENTREZ_FETCH = "efetch.fcgi"
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function fetch(ids::AbstractString...)
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url = ENTREZ_BASE_URL * ENTREZ_FETCH * "?db=nuccore&id=" * join(ids, ",") * "&rettype=fasta&retmode=text"
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path = Downloads.download(url)
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records = FASTA.Record[]
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open(FASTA.Reader, path) do reader
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record = FASTA.Record()
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while !eof(f)
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read!(f, record)
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push!(records, record)
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end
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end
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return records
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end
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end

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