Updated for BioSequences v2.0.0

Manifest.toml

@@ -1,49 +1,37 @@
 # This file is machine-generated - editing it directly is not advised
 
 [[Automa]]
-deps = ["DataStructures", "Printf", "Random", "Test", "TranscodingStreams"]
-git-tree-sha1 = "c81526bf5f6fb4616b4e22a3cd62ac20e255fd3c"
+deps = ["DataStructures", "Printf", "Test", "TranscodingStreams"]
+git-tree-sha1 = "1b1defa8b36d44dd22c715b5c884c8f795eea7fe"
 uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
-version = "0.8.0"
+version = "0.7.0"
 
 [[Base64]]
 uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"
 
-[[BioCore]]
-deps = ["Automa", "BufferedStreams", "YAML"]
-git-tree-sha1 = "476edbf4ef94594fff430a84ca96f86cb2327a71"
-uuid = "37cfa864-2cd6-5c12-ad9e-b6597d696c81"
-version = "2.0.5"
+[[BioGenerics]]
+deps = ["TranscodingStreams"]
+git-tree-sha1 = "57deb413ca9f4c8bc7d4c6e98ebe217ff728c737"
+uuid = "47718e42-2ac5-11e9-14af-e5595289c2ea"
+version = "0.1.0"
 
 [[BioSequences]]
-deps = ["Automa", "BioCore", "BioSymbols", "BufferedStreams", "Combinatorics", "IndexableBitVectors", "IntervalTrees", "LinearAlgebra", "Printf", "Random", "Test", "Twiddle"]
-git-tree-sha1 = "29341326bfab7ebef261dab128874b9e3fece5c2"
+deps = ["BioGenerics", "BioSymbols", "Combinatorics", "IndexableBitVectors", "Printf", "Random", "Twiddle"]
+git-tree-sha1 = "e5885ab9f665bffdd1a9b7b50c92f670ece31490"
 uuid = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
-version = "1.1.0"
+version = "2.0.0"
 
 [[BioSymbols]]
-deps = ["Automa", "Test"]
-git-tree-sha1 = "36bd8fc32e02b60dba123d5eecc7b4a90ef7d265"
+deps = ["Automa"]
+git-tree-sha1 = "c5bc104ddb3088fa698481a2fe92a1b1c1b6db77"
 uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
-version = "3.1.0"
-
-[[BufferedStreams]]
-deps = ["Compat", "Test"]
-git-tree-sha1 = "5d55b9486590fdda5905c275bb21ce1f0754020f"
-uuid = "e1450e63-4bb3-523b-b2a4-4ffa8c0fd77d"
-version = "1.0.0"
+version = "4.0.1"
 
 [[CategoricalArrays]]
-deps = ["Compat", "Future", "JSON", "Missings", "Printf", "Reexport"]
-git-tree-sha1 = "26601961df6afacdd16d67c1eec6cfe75e5ae9ab"
+deps = ["Compat", "DataAPI", "Future", "JSON", "Missings", "Printf", "Reexport"]
+git-tree-sha1 = "13240cfcc884837fc1aa89b60d500a652bcc3f10"
 uuid = "324d7699-5711-5eae-9e2f-1d82baa6b597"
-version = "0.5.4"
-
-[[Codecs]]
-deps = ["Test"]
-git-tree-sha1 = "70885e5e038cba1c4c17a84ad6c40756e10a4fb5"
-uuid = "19ecbf4d-ef7c-5e4b-b54a-0a0ff23c5aed"
-version = "0.5.0"
+version = "0.5.5"
 
 [[Combinatorics]]
 deps = ["LinearAlgebra", "Polynomials", "Test"]
@@ -57,11 +45,16 @@ git-tree-sha1 = "84aa74986c5b9b898b0d1acaf3258741ee64754f"
 uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
 version = "2.1.0"
 
+[[DataAPI]]
+git-tree-sha1 = "891a09f4f90361a28d0391c104a65c0202e22624"
+uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
+version = "1.0.0"
+
 [[DataFrames]]
-deps = ["CategoricalArrays", "Compat", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "StatsBase", "TableTraits", "Tables", "Unicode"]
-git-tree-sha1 = "def266a7e5eb6f633ef4c72633d2a328b9450052"
+deps = ["CategoricalArrays", "Compat", "DataAPI", "InvertedIndices", "IteratorInterfaceExtensions", "Missings", "PooledArrays", "Printf", "REPL", "Reexport", "SortingAlgorithms", "Statistics", "TableTraits", "Tables", "Unicode"]
+git-tree-sha1 = "12a96f70fc126f8a308eadd4eda843dfa630bbd4"
 uuid = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
-version = "0.19.0"
+version = "0.19.1"
 
 [[DataStructures]]
 deps = ["InteractiveUtils", "OrderedCollections"]
@@ -106,12 +99,6 @@ version = "1.0.0"
 deps = ["Markdown"]
 uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"
 
-[[IntervalTrees]]
-deps = ["InteractiveUtils", "Profile", "Random", "Test"]
-git-tree-sha1 = "6c9fcd87677231ae293f6806fad928c216ab6658"
-uuid = "524e6230-43b7-53ae-be76-1e9e4d08d11b"
-version = "1.0.0"
-
 [[InvertedIndices]]
 deps = ["Test"]
 git-tree-sha1 = "15732c475062348b0165684ffe28e85ea8396afc"
@@ -124,10 +111,10 @@ uuid = "82899510-4779-5014-852e-03e436cf321d"
 version = "1.0.0"
 
 [[JSON]]
-deps = ["Dates", "Distributed", "Mmap", "Sockets", "Test", "Unicode"]
-git-tree-sha1 = "1f7a25b53ec67f5e9422f1f551ee216503f4a0fa"
+deps = ["Dates", "Mmap", "Parsers", "Unicode"]
+git-tree-sha1 = "b34d7cef7b337321e97d22242c3c2b91f476748e"
 uuid = "682c06a0-de6a-54ab-a142-c8b1cf79cde6"
-version = "0.20.0"
+version = "0.21.0"
 
 [[LibGit2]]
 uuid = "76f85450-5226-5b5a-8eaa-529ad045b433"
@@ -161,6 +148,12 @@ git-tree-sha1 = "c4c13474d23c60d20a67b217f1d7f22a40edf8f1"
 uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
 version = "1.1.0"
 
+[[Parsers]]
+deps = ["Dates", "Test"]
+git-tree-sha1 = "db2b35dedab3c0e46dc15996d170af07a5ab91c9"
+uuid = "69de0a69-1ddd-5017-9359-2bf0b02dc9f0"
+version = "0.3.6"
+
 [[Pkg]]
 deps = ["Dates", "LibGit2", "Markdown", "Printf", "REPL", "Random", "SHA", "UUIDs"]
 uuid = "44cfe95a-1eb2-52ea-b672-e2afdf69b78f"
@@ -180,10 +173,6 @@ version = "0.5.2"
 deps = ["Unicode"]
 uuid = "de0858da-6303-5e67-8744-51eddeeeb8d7"
 
-[[Profile]]
-deps = ["Printf"]
-uuid = "9abbd945-dff8-562f-b5e8-e1ebf5ef1b79"
-
 [[REPL]]
 deps = ["InteractiveUtils", "Markdown", "Sockets"]
 uuid = "3fa0cd96-eef1-5676-8a61-b3b8758bbffb"
@@ -198,12 +187,6 @@ git-tree-sha1 = "7b1d07f411bc8ddb7977ec7f377b97b158514fe0"
 uuid = "189a3867-3050-52da-a836-e630ba90ab69"
 version = "0.2.0"
 
-[[Requires]]
-deps = ["Test"]
-git-tree-sha1 = "f6fbf4ba64d295e146e49e021207993b6b48c7d1"
-uuid = "ae029012-a4dd-5104-9daa-d747884805df"
-version = "0.5.2"
-
 [[SHA]]
 uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
 
@@ -231,49 +214,36 @@ uuid = "2f01184e-e22b-5df5-ae63-d93ebab69eaf"
 deps = ["LinearAlgebra", "SparseArrays"]
 uuid = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"
 
-[[StatsBase]]
-deps = ["DataStructures", "LinearAlgebra", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics"]
-git-tree-sha1 = "2b6ca97be7ddfad5d9f16a13fe277d29f3d11c23"
-uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
-version = "0.31.0"
-
 [[TableTraits]]
 deps = ["IteratorInterfaceExtensions"]
 git-tree-sha1 = "b1ad568ba658d8cbb3b892ed5380a6f3e781a81e"
 uuid = "3783bdb8-4a98-5b6b-af9a-565f29a5fe9c"
 version = "1.0.0"
 
 [[Tables]]
-deps = ["DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "Requires", "TableTraits", "Test"]
-git-tree-sha1 = "2e5d1a0d9b574ee2ed0c1a2fe32807de022376dd"
+deps = ["DataAPI", "DataValueInterfaces", "IteratorInterfaceExtensions", "LinearAlgebra", "TableTraits", "Test"]
+git-tree-sha1 = "951b5be359e92703f886881b175ecfe924d8bd91"
 uuid = "bd369af6-aec1-5ad0-b16a-f7cc5008161c"
-version = "0.2.9"
+version = "0.2.10"
 
 [[Test]]
 deps = ["Distributed", "InteractiveUtils", "Logging", "Random"]
 uuid = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [[TranscodingStreams]]
 deps = ["Random", "Test"]
-git-tree-sha1 = "a25d8e5a28c3b1b06d3859f30757d43106791919"
+git-tree-sha1 = "7c53c35547de1c5b9d46a4797cf6d8253807108c"
 uuid = "3bb67fe8-82b1-5028-8e26-92a6c54297fa"
-version = "0.9.4"
+version = "0.9.5"
 
 [[Twiddle]]
-deps = ["Test"]
-git-tree-sha1 = "45a81952077aaf0396c3ddcbd561e660a44ce331"
+git-tree-sha1 = "475f0c0e1633b51e81cf92099356fcb4029a9e19"
 uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
-version = "1.1.0"
+version = "1.1.1"
 
 [[UUIDs]]
 deps = ["Random", "SHA"]
 uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"
 
 [[Unicode]]
 uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"
-
-[[YAML]]
-deps = ["Codecs", "Compat"]
-git-tree-sha1 = "3bde77cee95cce0c0b9b18813d85e18e8ed4f415"
-uuid = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
-version = "0.3.2"

Project.toml

@@ -8,12 +8,12 @@ BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
 GZip = "92fee26a-97fe-5a0c-ad85-20a5f3185b63"
 
+[compat]
+DataFrames = "0.19.0"
+julia = "1"
+
 [extras]
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
 
 [targets]
 test = ["Test"]
-
-[compat]
-julia = "1"
-DataFrames = "0.19.0"

src/readgbk.jl

@@ -32,7 +32,7 @@ end
 
 
 """
-Parse footer (sequence) portion of a GenBank file, returning a `String`. When `BioSequences` is available for 0.7 this will be changed to a `DNASequence`.
+Parse footer (sequence) portion of a GenBank file, returning a `String`.
 """
 function filterseq(io::IOBuffer)
     line = String(take!(io))
@@ -162,7 +162,7 @@ function parsechromosome(lines)
         end
     end
     chromosome.name = parseheader(chromosome.header)
-    chromosome.sequence = DNASequence(filterseq(iobuffer))
+    chromosome.sequence = LongDNASeq(filterseq(iobuffer))
     return linecount, chromosome
 end
 

src/types.jl

@@ -37,7 +37,7 @@ end
 
 mutable struct Chromosome{G <: AbstractGene}
     name::String
-    sequence::DNASequence
+    sequence::LongDNASeq
     header::String
     genes::Vector{G}
     genedata::DataFrame
@@ -211,7 +211,7 @@ end
 
 Return genomic sequence for `gene`.
 """
-function BioSequences.sequence(gene::AbstractGene)
+function sequence(gene::AbstractGene)
     ifelse(gene.locus.strand == '-',
         reverse_complement(gene.parent.sequence[gene.parent.genedata[gene.index, :locus].position]),
         gene.parent.sequence[gene.parent.genedata[gene.index, :locus].position])