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docs: update docstring of some methods
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camilogarciabotero committed Jul 4, 2024
1 parent 3ecc68c commit 53efdd4
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6 changes: 3 additions & 3 deletions src/findorfs.jl
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@@ -1,14 +1,14 @@
export findorfs

"""
findorfs(sequence::NucleicSeqOrView{DNAAlphabet{N}}; ::M, kwargs...) where {N, M<:GeneFinderMethod}
findorfs(sequence::NucleicSeqOrView{DNAAlphabet{N}}; ::F, kwargs...) where {N, F<:GeneFinderMethod}
This is the main interface method for finding open reading frames (ORFs) in a DNA sequence.
It takes the following required arguments:
- `sequence`: The nucleic acid sequence to search for ORFs.
- `method`: The algorithm used to find ORFs. It can be either `NaiveFinder()`, `NaiveFinderScored()` or yet other implementations.
- `finder`: The algorithm used to find ORFs. It can be either `NaiveFinder`, `NaiveCollector` or yet other implementations.
## Keyword Arguments regardless of the finder method:
- `alternative_start::Bool`: A boolean indicating whether to consider alternative start codons. Default is `false`.
Expand All @@ -26,7 +26,7 @@ sequence = randdnaseq(120)
120nt DNA Sequence:
GCCGGACAGCGAAGGCTAATAAATGCCCGTGCCAGTATC…TCTGAGTTACTGTACACCCGAAAGACGTTGTACGCATTT
findorfs(sequence, NaiveFinder())
findorfs(sequence, finder=NaiveFinder)
1-element Vector{ORF}:
ORF{NaiveFinder}(77:118, '-', 2, 0.0)
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6 changes: 3 additions & 3 deletions src/types.jl
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Expand Up @@ -42,7 +42,7 @@ The `ORF` struct represents an Open Reading Frame (ORF) in genomics.
- `features::Features`: The features associated with the ORF.
- `scheme::Union{Nothing,Function}`: The scheme used for the ORF.
# Constructor
# Main Constructor
```julia
ORF{N,F}(
Expand All @@ -54,7 +54,7 @@ ORF{N,F}(
features::Features,
scheme::Union{Nothing,Function}
)
```
# Example
A full instance `ORF`
Expand Down Expand Up @@ -194,7 +194,7 @@ Extracts the features from an `ORF` object.
- `i::ORF{N,F}`: An `ORF` object.
# Returns
The features of the `ORF` object.
The features of the `ORF` object. Those could be defined by each `GeneFinderMethod`.
"""
function features(i::ORF{N,F}) where {N,F}
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