Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Refactor ORF main type, update entire writting API and other general changes #23

Merged
merged 42 commits into from
Jan 10, 2024
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
42 commits
Select commit Hold shift + click to select a range
e37d83a
Update dependencies in Manifest.toml
camilogarciabotero Jan 5, 2024
48bd298
Add NucleicSeqOrView to BioSequences import
camilogarciabotero Jan 5, 2024
e779a78
Refactor gene structs and update types
camilogarciabotero Jan 5, 2024
b0c65f4
Refactor nucleotidefreqs and hasprematurestop functions
camilogarciabotero Jan 5, 2024
777c858
Refactor findorfs.jl to use NucleicSeqOrView type
camilogarciabotero Jan 5, 2024
b18d386
Refactor getorfdna function in findorfs.jl
camilogarciabotero Jan 5, 2024
8291805
Add ncbi_trans_table and translate functions to GeneFinder.jl
camilogarciabotero Jan 5, 2024
86cf036
Optimize findorfs and getorfdna functions
camilogarciabotero Jan 8, 2024
c432bca
Remove unnecessary export statement
camilogarciabotero Jan 8, 2024
7fc2612
Update docs with new API renaming
camilogarciabotero Jan 8, 2024
bdb71dc
Refactor function names and add new function to record DNA ORFs
camilogarciabotero Jan 8, 2024
c520cee
Fix newline issue in GeneFinder.jl
camilogarciabotero Jan 8, 2024
7392073
Update write_orfs_aa to write_orfs_faa
camilogarciabotero Jan 9, 2024
f16b96a
Refactor sort and getindex functions in extended.jl
camilogarciabotero Jan 9, 2024
cc2d8a5
Refactor ORF printing in write_orfs_fna, write_orfs_faa, and write_or…
camilogarciabotero Jan 9, 2024
655108f
Refactor frame type in ORF struct
camilogarciabotero Jan 9, 2024
ff6b24e
Update function parameter type in hasprematurestop()
camilogarciabotero Jan 9, 2024
f64ab97
Refactor get_orfs_dna and get_orfs_aa methods
camilogarciabotero Jan 9, 2024
b0b3ece
Add newline
camilogarciabotero Jan 9, 2024
c50d9e0
Update dependencies and import statements and add Aqua tests
camilogarciabotero Jan 9, 2024
da52bd1
Fix findorfstest and io.jl
camilogarciabotero Jan 9, 2024
7c210ed
Refactor write_orfs_bed and write_orfs_gff functions
camilogarciabotero Jan 9, 2024
bd14f17
Update write_orfs_bed and write_orfs_gff functions
camilogarciabotero Jan 9, 2024
bf71305
Delete unused references and documentation files
camilogarciabotero Jan 10, 2024
bb42ff7
Update frame field type in ORF struct
camilogarciabotero Jan 10, 2024
c5440b6
Add RNA support to locationiterator function
camilogarciabotero Jan 10, 2024
318d7f4
Add RNAAlphabet to BioSequences
camilogarciabotero Jan 10, 2024
a22939a
Update dependencies and add new documentation files
camilogarciabotero Jan 10, 2024
badaa30
Remove commented out code and update documentation
camilogarciabotero Jan 10, 2024
e257f20
Add RNAAlphabet to BioSequences
camilogarciabotero Jan 10, 2024
23b4732
Update dependencies and add new documentation files
camilogarciabotero Jan 10, 2024
d702fe4
Remove commented out code and update documentation
camilogarciabotero Jan 10, 2024
54ef1de
Merge branch 'dev' of https://github.com/camilogarciabotero/GeneFinde…
camilogarciabotero Jan 10, 2024
44aed4a
Revert the RNAlphabet type in all cases
camilogarciabotero Jan 10, 2024
c9ffec0
Update CHANGELOG.md and bump version to 0.2.0
camilogarciabotero Jan 10, 2024
cd2830d
Refactor ORF writing functions and improve ORF type validation in docs
camilogarciabotero Jan 10, 2024
1f17190
Add support for writing protein sequences from a string input
camilogarciabotero Jan 10, 2024
0c98b38
Add Aqua QA badge
camilogarciabotero Jan 10, 2024
3a220cc
Update ORF finding and writing functions in README.md
camilogarciabotero Jan 10, 2024
b260a5f
Add ORF sequences to output file
camilogarciabotero Jan 10, 2024
7240c1e
Fix typo in README and documentation
camilogarciabotero Jan 10, 2024
6ce48ff
Add functions to write ORFs to different file formats
camilogarciabotero Jan 10, 2024
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
13 changes: 10 additions & 3 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -6,9 +6,16 @@ The format is based on Keep a Changelog and this project adheres to Semantic Ver

## [UNRELEASED](https://github.com/camilogarciabotero/GeneFinder.jl/compare/v0.0.10...main)

- Add `write_gff` methods.
- Clean up comments and docs.
- Add `iscoding` method.

## [0.2.0]

- A more stable ORF type that asserts for incorrect ORFs.
- Extended `Base.getindex` method to better handle ORF enabling: `seq[orf]` regardless of the ORF strand.
- The `write_*` API is much more stable and its been rewriten to handle IOStreams and `IOBuffers` as well.
- The new `record_orfs_fna` and `record_orfs_faa` methods intearact with the FASTX interface.
- Codebase has been reduced. Direct String manipulation is not enabled for `findorfs` and `get_*` methods.
- Docstrings have been updated following method updates.
- Better tests and now `Aqua.jl` is used for several tests as well.

## [0.1.0]

Expand Down
187 changes: 3 additions & 184 deletions Manifest.toml
Original file line number Diff line number Diff line change
Expand Up @@ -2,40 +2,20 @@

julia_version = "1.10.0"
manifest_format = "2.0"
project_hash = "5f5bec69be3c8dc8bff8fce86338a1ef1e8ac046"

[[deps.Artifacts]]
uuid = "56f22d72-fd6d-98f1-02f0-08ddc0907c33"
project_hash = "4f6774eaeaec568c8cb7a865a84c0c7d9a180727"

[[deps.Automa]]
deps = ["PrecompileTools", "TranscodingStreams"]
git-tree-sha1 = "0da671c730d79b8f9a88a391556ec695ea921040"
uuid = "67c07d97-cdcb-5c2c-af73-a7f9c32a568b"
version = "1.0.2"

[[deps.Base64]]
uuid = "2a0f44e3-6c83-55bd-87e4-b1978d98bd5f"

[[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 = "44da2d71c2e9a68babb324c4df69d87b9ff7a835"
uuid = "f861b655-cb5f-42ce-b66a-341b542d4f2c"
version = "0.9.0"

[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"]
git-tree-sha1 = "6fdba8b4279460fef5674e9aa2dac7ef5be361d5"
Expand All @@ -48,42 +28,10 @@ git-tree-sha1 = "e32a61f028b823a172c75e26865637249bb30dff"
uuid = "3c28c6f8-a34d-59c4-9654-267d177fcfa9"
version = "5.1.3"

[[deps.Compat]]
deps = ["UUIDs"]
git-tree-sha1 = "886826d76ea9e72b35fcd000e535588f7b60f21d"
uuid = "34da2185-b29b-5c13-b0c7-acf172513d20"
version = "4.10.1"
weakdeps = ["Dates", "LinearAlgebra"]

[deps.Compat.extensions]
CompatLinearAlgebraExt = "LinearAlgebra"

[[deps.CompilerSupportLibraries_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "e66e0078-7015-5450-92f7-15fbd957f2ae"
version = "1.0.5+1"

[[deps.DataAPI]]
git-tree-sha1 = "8da84edb865b0b5b0100c0666a9bc9a0b71c553c"
uuid = "9a962f9c-6df0-11e9-0e5d-c546b8b5ee8a"
version = "1.15.0"

[[deps.DataStructures]]
deps = ["Compat", "InteractiveUtils", "OrderedCollections"]
git-tree-sha1 = "3dbd312d370723b6bb43ba9d02fc36abade4518d"
uuid = "864edb3b-99cc-5e75-8d2d-829cb0a9cfe8"
version = "0.18.15"

[[deps.Dates]]
deps = ["Printf"]
uuid = "ade2ca70-3891-5945-98fb-dc099432e06a"

[[deps.DocStringExtensions]]
deps = ["LibGit2"]
git-tree-sha1 = "2fb1e02f2b635d0845df5d7c167fec4dd739b00d"
uuid = "ffbed154-4ef7-542d-bbb7-c09d3a79fcae"
version = "0.9.3"

[[deps.FASTX]]
deps = ["Automa", "BioGenerics", "PrecompileTools", "StringViews", "TranscodingStreams"]
git-tree-sha1 = "bff5d62bf5e1c382a370ac701bcaea9a24115ac6"
Expand All @@ -94,85 +42,10 @@ weakdeps = ["BioSequences"]
[deps.FASTX.extensions]
BioSequencesExt = "BioSequences"

[[deps.InteractiveUtils]]
deps = ["Markdown"]
uuid = "b77e0a4c-d291-57a0-90e8-8db25a27a240"

[[deps.IrrationalConstants]]
git-tree-sha1 = "630b497eafcc20001bba38a4651b327dcfc491d2"
uuid = "92d709cd-6900-40b7-9082-c6be49f344b6"
version = "0.2.2"

[[deps.IterTools]]
git-tree-sha1 = "274c38bd733f9d29036d0a73658fff1dc1d3a065"
git-tree-sha1 = "42d5f897009e7ff2cf88db414a389e5ed1bdd023"
uuid = "c8e1da08-722c-5040-9ed9-7db0dc04731e"
version = "1.9.0"

[[deps.LibGit2]]
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"
version = "1.11.0+1"

[[deps.Libdl]]
uuid = "8f399da3-3557-5675-b5ff-fb832c97cbdb"

[[deps.LinearAlgebra]]
deps = ["Libdl", "OpenBLAS_jll", "libblastrampoline_jll"]
uuid = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"

[[deps.LogExpFunctions]]
deps = ["DocStringExtensions", "IrrationalConstants", "LinearAlgebra"]
git-tree-sha1 = "7d6dd4e9212aebaeed356de34ccf262a3cd415aa"
uuid = "2ab3a3ac-af41-5b50-aa03-7779005ae688"
version = "0.3.26"

[deps.LogExpFunctions.extensions]
LogExpFunctionsChainRulesCoreExt = "ChainRulesCore"
LogExpFunctionsChangesOfVariablesExt = "ChangesOfVariables"
LogExpFunctionsInverseFunctionsExt = "InverseFunctions"

[deps.LogExpFunctions.weakdeps]
ChainRulesCore = "d360d2e6-b24c-11e9-a2a3-2a2ae2dbcce4"
ChangesOfVariables = "9e997f8a-9a97-42d5-a9f1-ce6bfc15e2c0"
InverseFunctions = "3587e190-3f89-42d0-90ee-14403ec27112"

[[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+1"

[[deps.Missings]]
deps = ["DataAPI"]
git-tree-sha1 = "f66bdc5de519e8f8ae43bdc598782d35a25b1272"
uuid = "e1d29d7a-bbdc-5cf2-9ac0-f12de2c33e28"
version = "1.1.0"

[[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 = "0.3.23+2"

[[deps.OrderedCollections]]
git-tree-sha1 = "dfdf5519f235516220579f949664f1bf44e741c5"
uuid = "bac558e1-5e72-5ebc-8fee-abe8a469f55d"
version = "1.6.3"
version = "1.10.0"

[[deps.PrecompileTools]]
deps = ["Preferences"]
Expand All @@ -198,47 +71,11 @@ uuid = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
uuid = "ea8e919c-243c-51af-8825-aaa63cd721ce"
version = "0.7.0"

[[deps.Serialization]]
uuid = "9e88b42a-f829-5b0c-bbe9-9e923198166b"

[[deps.SortingAlgorithms]]
deps = ["DataStructures"]
git-tree-sha1 = "66e0a8e672a0bdfca2c3f5937efb8538b9ddc085"
uuid = "a2af1166-a08f-5f64-846c-94a0d3cef48c"
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 = "1.10.0"

[[deps.StatsAPI]]
deps = ["LinearAlgebra"]
git-tree-sha1 = "1ff449ad350c9c4cbc756624d6f8a8c3ef56d3ed"
uuid = "82ae8749-77ed-4fe6-ae5f-f523153014b0"
version = "1.7.0"

[[deps.StatsBase]]
deps = ["DataAPI", "DataStructures", "LinearAlgebra", "LogExpFunctions", "Missings", "Printf", "Random", "SortingAlgorithms", "SparseArrays", "Statistics", "StatsAPI"]
git-tree-sha1 = "1d77abd07f617c4868c33d4f5b9e1dbb2643c9cf"
uuid = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"
version = "0.34.2"

[[deps.StringViews]]
git-tree-sha1 = "f7b06677eae2571c888fd686ba88047d8738b0e3"
uuid = "354b36f9-a18e-4713-926e-db85100087ba"
version = "1.3.3"

[[deps.SuiteSparse_jll]]
deps = ["Artifacts", "Libdl", "libblastrampoline_jll"]
uuid = "bea87d4a-7f5b-5778-9afe-8cc45184846c"
version = "7.2.1+1"

[[deps.TOML]]
deps = ["Dates"]
uuid = "fa267f1f-6049-4f14-aa54-33bafae1ed76"
Expand All @@ -261,23 +98,5 @@ git-tree-sha1 = "29509c4862bfb5da9e76eb6937125ab93986270a"
uuid = "7200193e-83a8-5a55-b20d-5d36d44a0795"
version = "1.1.2"

[[deps.UUIDs]]
deps = ["Random", "SHA"]
uuid = "cf7118a7-6976-5b1a-9a39-7adc72f591a4"

[[deps.Unicode]]
uuid = "4ec0a83e-493e-50e2-b9ac-8f72acf5a8f5"

[[deps.VectorizedKmers]]
git-tree-sha1 = "eaf497f1b720ae17dc52463dfe5fed5f74b0e4df"
uuid = "2ef45bd6-4c2b-43d8-88b3-40597287359a"
version = "0.8.1"
weakdeps = ["BioSequences"]

[deps.VectorizedKmers.extensions]
BioSequencesExt = "BioSequences"

[[deps.libblastrampoline_jll]]
deps = ["Artifacts", "Libdl"]
uuid = "8e850b90-86db-534c-a0d3-1478176c7d93"
version = "5.8.0+1"
9 changes: 3 additions & 6 deletions Project.toml
Original file line number Diff line number Diff line change
@@ -1,27 +1,24 @@
name = "GeneFinder"
uuid = "2bc6ee46-2158-4f5a-a720-91cb2d7cee64"
authors = ["Camilo García-Botero"]
version = "0.1.0"
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"
StatsBase = "2913bbd2-ae8a-5f71-8c99-4fb6c76f3a91"

[compat]
BioMarkovChains = "0.9.0"
BioSequences = "3"
FASTX = "2"
IterTools = "1.4"
PrecompileTools = "1"
StatsBase = "0.34.0"
julia = "1"

[extras]
Aqua = "4c88cf16-eb10-579e-8560-4a9242c79595"
Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40"

[targets]
test = ["Test"]
test = ["Test", "Aqua"]
Loading
Loading