Moving ORF as an AbstractGenomicInterval{T}

.github/workflows/CI.yml

@@ -35,11 +35,11 @@ jobs:
  with:
  version: ${{ matrix.version }}
  arch: ${{ matrix.arch }}
- - uses: julia-actions/cache@v1
+ - uses: julia-actions/cache@v2
  - uses: julia-actions/julia-buildpkg@v1
  - uses: julia-actions/julia-runtest@v1
  - uses: julia-actions/julia-processcoverage@v1
- - uses: codecov/codecov-action@v3
+ - uses: codecov/codecov-action@v4
  with:
  files: lcov.info
  docs:

.gitignore

@@ -5,4 +5,5 @@
 .travis.yml
 /docs/src/*_cache
 /docs/src/*_files
-/test/Manifest.toml
+/test/Manifest.toml
+Manifest.toml

Project.toml

@@ -7,20 +7,25 @@ version = "0.4.0"
 BioMarkovChains = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
 BioSequences = "7e6ae17a-c86d-528c-b3b9-7f778a29fe59"
 FASTX = "c2308a5c-f048-11e8-3e8a-31650f418d12"
+GenomicFeatures = "899a7d2d-5c61-547b-bef9-6698a8d05446"
 IterTools = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
 PrecompileTools = "aea7be01-6a6a-4083-8856-8a6e6704d82a"
 
 [compat]
-BioMarkovChains = "0.9"
+BioMarkovChains = "0.10"
 BioSequences = "3"
 FASTX = "2"
+GenomicFeatures = "3"
 IterTools = "1.4"
 PrecompileTools = "1"
-julia = "1"
+julia = "1.6"
 
 [extras]
 Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
+LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
+StyledStrings = "f489334b-da3d-4c2e-b8f0-e476e12c162b"
 Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"
+YAML = "ddb6d928-2868-570f-bddf-ab3f9cf99eb6"
 
 [targets]
-test = ["Test", "Aqua"]
+test = ["Test", "Aqua", "LinearAlgebra", "StyledStrings", "YAML"]

README.md

@@ -50,27 +50,27 @@ seq = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCA
 Now lest us find the ORFs
 
 ```julia
-findorfs(seq, NaiveFinder())
-
-12-element Vector{ORF}:
- ORF(29:40, '+', 2, 0.0)
- ORF(137:145, '+', 2, 0.0)
- ORF(164:184, '+', 2, 0.0)
- ORF(173:184, '+', 2, 0.0)
- ORF(236:241, '+', 2, 0.0)
- ORF(248:268, '+', 2, 0.0)
- ORF(362:373, '+', 2, 0.0)
- ORF(470:496, '+', 2, 0.0)
- ORF(551:574, '+', 2, 0.0)
- ORF(569:574, '+', 2, 0.0)
- ORF(581:601, '+', 2, 0.0)
- ORF(695:706, '+', 2, 0.0)
+orfs = findorfs(seq, finder=NaiveFinder) # use finder=NaiveCollector as an alternative
+
+12-element Vector{ORF{4, NaiveFinder}}:
+ ORF{NaiveFinder}(29:40, '+', 2)
+ ORF{NaiveFinder}(137:145, '+', 2)
+ ORF{NaiveFinder}(164:184, '+', 2)
+ ORF{NaiveFinder}(173:184, '+', 2)
+ ORF{NaiveFinder}(236:241, '+', 2)
+ ORF{NaiveFinder}(248:268, '+', 2)
+ ORF{NaiveFinder}(362:373, '+', 2)
+ ORF{NaiveFinder}(470:496, '+', 2)
+ ORF{NaiveFinder}(551:574, '+', 2)
+ ORF{NaiveFinder}(569:574, '+', 2)
+ ORF{NaiveFinder}(581:601, '+', 2)
+ ORF{NaiveFinder}(695:706, '+', 2)
 ```
 
-Two other methods where implemented into `getorfs` to get the ORFs in DNA or aminoacid sequences, respectively. They use the `findorfs` function to first get the ORFs and then get the correspondance array of `BioSequence` objects.
+The `ORF` structure contains also the sequence of the ORF, the frame, and several features. If you want to get the sequence of the ORFs you can broadcast the `sequence` function to safely extract the sequences of all ORFs.
 
 ```julia
-getorfs(seq, DNAAlphabet{4}(), NaiveFinder())
+sequence.(orfs)
 
 12-element Vector{LongSubSeq{DNAAlphabet{4}}}:
  ATGCAACCCTGA
@@ -87,6 +87,26 @@ getorfs(seq, DNAAlphabet{4}(), NaiveFinder())
  ATGCAACCCTGA
 ```
 
+Similarly, you can extract the amino acid sequences of the ORFs using the `translate` function.
+
+```julia
+translate.(orfs)
+
+12-element Vector{LongAA}:
+ MQP*
+ MR*
+ MRRMAR*
+ MAR*
+ M*
+ MCPTAV*
+ MQP*
+ MHWLVLSI*
+ MSPHKAM*
+ M*
+ MCPTAA*
+ MQP*
+```
+
 ## Writting ORF information into bioinformatic formats
 
 This package facilitates now the creation of `FASTA`, `BED`, and `GFF` files, specifically extracting Open Reading Frame (ORF) information from `BioSequence` instances, particularly those of type `NucleicSeqOrView{A} where A`, and then writing the information into the desired format.
@@ -118,7 +138,7 @@ Once a `BioSequence` object has been instantiated, the `write_orfs_fna` function
 outfile = "LFLS01000089.fna"
 
 open(outfile, "w") do io
- write_orfs_fna(seq, io, NaiveFinder())
+ write_orfs_fna(seq, io, finder=NaiveFinder) # use finder=NaiveCollector as an alternative
 end
 ```