Add 'Get Started' guide for finding ORFIs and update documentation na…

…vigation

docs/getstarterd.md

@@ -0,0 +1,71 @@
+## Finding complete and overlapped ORFIs
+
+The main package function is `findorfs`. Under the hood, the `findorfs` function is an interface for different gene finding algorithms that can be plugged using the `finder` keyword argument. By default it uses the `NaiveFinder` algorithm, which is a simple algorithm that finds all (non-outbounded) ORFIs in a DNA sequence (see the [NaiveFinder](https://camilogarciabotero.github.io/GeneFinder.jl/dev/api/#GeneFinder.NaiveFinder-Union{Tuple{Union{BioSequences.LongDNA{N},%20BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}},%20Tuple{N}}%20where%20N) documentation for more details).
+
+> [!NOTE] 
+  The `minlen` kwarg in the `NaiveFinder` mehtod has been set to 6nt, so it will catch random ORFIs not necesarily genes thus it might consider `dna"ATGTGA"` -> `aa"M*"` as a plausible ORFI.
+
+Here is an example of how to use the `findorfs` function with the `NaiveFinder` algorithm:
+
+```julia
+using BioSequences, GeneFinder
+
+# > 180195.SAMN03785337.LFLS01000089 -> finds only 1 gene in Prodigal (from Pyrodigal tests)
+seq = dna"AACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAACAGCACTGGCAATCTGACTGTGGGCGGTGTTACCAACGGCACTGCTACTACTGGCAACATCGCACTGACCGGTAACAATGCGCTGAGCGGTCCGGTCAATCTGAATGCGTCGAATGGCACGGTGACCTTGAACACGACCGGCAATACCACGCTCGGTAACGTGACGGCACAAGGCAATGTGACGACCAATGTGTCCAACGGCAGTCTGACGGTTACCGGCAATACGACAGGTGCCAACACCAACCTCAGTGCCAGCGGCAACCTGACCGTGGGTAACCAGGGCAATATCAGTACCGCAGGCAATGCAACCCTGACGGCCGGCGACAACCTGACGAGCACTGGCAATCTGACTGTGGGCGGCGTCACCAACGGCACGGCCACCACCGGCAACATCGCGCTGACCGGTAACAATGCACTGGCTGGTCCTGTCAATCTGAACGCGCCGAACGGCACCGTGACCCTGAACACAACCGGCAATACCACGCTGGGTAATGTCACCGCACAAGGCAATGTGACGACTAATGTGTCCAACGGCAGCCTGACAGTCGCTGGCAATACCACAGGTGCCAACACCAACCTGAGTGCCAGCGGCAATCTGACCGTGGGCAACCAGGGCAATATCAGTACCGCGGGCAATGCAACCCTGACTGCCGGCGGTAACCTGAGC"
+
+orfs = findorfs(seq, finder=NaiveFinder) # use finder=NaiveCollector as an alternative
+
+12-element Vector{ORFI{4, NaiveFinder}}:
+ ORFI{NaiveFinder}(29:40, '+', 2)
+ ORFI{NaiveFinder}(137:145, '+', 2)
+ ORFI{NaiveFinder}(164:184, '+', 2)
+ ORFI{NaiveFinder}(173:184, '+', 2)
+ ORFI{NaiveFinder}(236:241, '+', 2)
+ ORFI{NaiveFinder}(248:268, '+', 2)
+ ORFI{NaiveFinder}(362:373, '+', 2)
+ ORFI{NaiveFinder}(470:496, '+', 2)
+ ORFI{NaiveFinder}(551:574, '+', 2)
+ ORFI{NaiveFinder}(569:574, '+', 2)
+ ORFI{NaiveFinder}(581:601, '+', 2)
+ ORFI{NaiveFinder}(695:706, '+', 2)
+```
+
+The `ORFI` structure displays the location, frame, and strand, but currently does not include the sequence *per se*. To extract the sequence of an `ORFI` instance, you can use the `sequence` method directly on it, or you can also broadcast it over the `orfs` collection using the dot syntax `.`:
+
+```julia
+sequence.(orfs)
+
+12-element Vector{LongSubSeq{DNAAlphabet{4}}}:
+ ATGCAACCCTGA
+ ATGCGCTGA
+ ATGCGTCGAATGGCACGGTGA
+ ATGGCACGGTGA
+ ATGTGA
+ ATGTGTCCAACGGCAGTCTGA
+ ATGCAACCCTGA
+ ATGCACTGGCTGGTCCTGTCAATCTGA
+ ATGTCACCGCACAAGGCAATGTGA
+ ATGTGA
+ ATGTGTCCAACGGCAGCCTGA
+ ATGCAACCCTGA
+```
+
+Similarly, you can extract the amino acid sequences of the ORFIs using the `translate` function.
+
+```julia
+translate.(orfs)
+
+12-element Vector{LongAA}:
+ MQP*
+ MR*
+ MRRMAR*
+ MAR*
+ M*
+ MCPTAV*
+ MQP*
+ MHWLVLSI*
+ MSPHKAM*
+ M*
+ MCPTAA*
+ MQP*
+```

docs/make.jl

@@ -38,6 +38,7 @@ fmt = DocumenterVitepress.MarkdownVitepress(
 
 pgs = [
     "Home" => "index.md",
+    "Get Started" => "getstarted.md",
     "Finding ORFs" => "naivefinder.md",
     "Scoring ORFs" => "features.md",
     "A Simple Coding Rule" => "simplecodingrule.md",