build based on c388afd

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-29T19:55:44","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-29T20:05:54","documenter_version":"1.5.0"}}

dev/api/index.html

@@ -44,4 +44,4 @@
 open(filename, "w") do file
      write_orfs_fna(seq, file, NaiveFinder())
 end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/camilogarciabotero/GeneFinder.jl/">source</a></section></article><article class="docstring"><header><a class="docstring-article-toggle-button fa-solid fa-chevron-down" href="javascript:;" title="Collapse docstring"></a><a class="docstring-binding" id="GeneFinder.write_orfs_gff-Union{Tuple{F}, Tuple{N}, Tuple{Union{BioSequences.LongDNA{N}, BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}, Union{IOStream, IOBuffer}}} where {N, F&lt;:GeneFinder.GeneFinderMethod}" href="#GeneFinder.write_orfs_gff-Union{Tuple{F}, Tuple{N}, Tuple{Union{BioSequences.LongDNA{N}, BioSequences.LongSubSeq{BioSequences.DNAAlphabet{N}}}, Union{IOStream, IOBuffer}}} where {N, F&lt;:GeneFinder.GeneFinderMethod}"><code>GeneFinder.write_orfs_gff</code></a> — <span class="docstring-category">Method</span></header><section><div><pre><code class="language-julia hljs">write_orfs_gff(input::NucleicSeqOrView{DNAAlphabet{N}}, output::Union{IOStream, IOBuffer}, finder::F; kwargs...)
-write_orfs_gff(input::NucleicSeqOrView{DNAAlphabet{N}}, output::String, finder::F; kwargs...)</code></pre><p>Write GFF data to a file.</p><p><strong>Arguments</strong></p><ul><li><code>input</code>: The input DNA sequence NucSeq or a view.</li><li><code>output</code>: The otput format, it can be a file (<code>String</code>) or a buffer (<code>IOStream</code> or `IOBuffer)</li><li><code>finder</code>: The algorithm used to find ORFs. It can be either <code>NaiveFinder()</code> or <code>NaiveFinderScored()</code>.</li></ul><p><strong>Keywords</strong></p><ul><li><code>code::GeneticCode=BioSequences.standard_genetic_code</code>: The genetic code by which codons will be translated. See <code>BioSequences.ncbi_trans_table</code> for more info. </li><li><code>alternative_start::Bool=false</code>: If true will pass the extended start codons to search. This will increase 3x the exec. time.</li><li><code>minlen::Int64=6</code>:  Length of the allowed ORF. Default value allow <code>aa&quot;M*&quot;</code> a posible encoding protein from the resulting ORFs.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/camilogarciabotero/GeneFinder.jl/">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../iodocs/">« Wrtiting ORFs In Files</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 19:55">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+write_orfs_gff(input::NucleicSeqOrView{DNAAlphabet{N}}, output::String, finder::F; kwargs...)</code></pre><p>Write GFF data to a file.</p><p><strong>Arguments</strong></p><ul><li><code>input</code>: The input DNA sequence NucSeq or a view.</li><li><code>output</code>: The otput format, it can be a file (<code>String</code>) or a buffer (<code>IOStream</code> or `IOBuffer)</li><li><code>finder</code>: The algorithm used to find ORFs. It can be either <code>NaiveFinder()</code> or <code>NaiveFinderScored()</code>.</li></ul><p><strong>Keywords</strong></p><ul><li><code>code::GeneticCode=BioSequences.standard_genetic_code</code>: The genetic code by which codons will be translated. See <code>BioSequences.ncbi_trans_table</code> for more info. </li><li><code>alternative_start::Bool=false</code>: If true will pass the extended start codons to search. This will increase 3x the exec. time.</li><li><code>minlen::Int64=6</code>:  Length of the allowed ORF. Default value allow <code>aa&quot;M*&quot;</code> a posible encoding protein from the resulting ORFs.</li></ul></div><a class="docs-sourcelink" target="_blank" href="https://github.com/camilogarciabotero/GeneFinder.jl/">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../iodocs/">« Wrtiting ORFs In Files</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 20:05">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/features/index.html

@@ -117,4 +117,4 @@
 
 axislegend(ax)
 
-f</code></pre><p><img src="../assets/lors-lambda.png" alt/></p><p>What this plot shows is that the ORFs in the lambda genome have a higher scores than random sequences of the same length. The score is a measure of how likely a sequence given the coding model is compared to the non-coding model. In other words, the higher the score the more likely the sequence is coding. So, the plot shows that the ORFs in the lambda genome are more likely to be coding regions than random sequences. It also shows that the longer the ORF the higher the score, which is expected since longer ORFs are more likely to be coding regions than shorter ones.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../naivefinder/">« Finding ORFs</a><a class="docs-footer-nextpage" href="../simplecodingrule/">A Simple Coding Rule »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 19:55">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+f</code></pre><p><img src="../assets/lors-lambda.png" alt/></p><p>What this plot shows is that the ORFs in the lambda genome have a higher scores than random sequences of the same length. The score is a measure of how likely a sequence given the coding model is compared to the non-coding model. In other words, the higher the score the more likely the sequence is coding. So, the plot shows that the ORFs in the lambda genome are more likely to be coding regions than random sequences. It also shows that the longer the ORF the higher the score, which is expected since longer ORFs are more likely to be coding regions than shorter ones.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../naivefinder/">« Finding ORFs</a><a class="docs-footer-nextpage" href="../simplecodingrule/">A Simple Coding Rule »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 20:05">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/index.html

@@ -41,4 +41,4 @@
 	version = {v0.3.0},
 	year    = {2024},
 	month   = {04}
-}</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="naivefinder/">Finding ORFs »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 19:55">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+}</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="naivefinder/">Finding ORFs »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 20:05">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/iodocs/index.html

@@ -31,4 +31,4 @@
 >seq id=11 start=581 stop=601 strand=+ frame=2 features=[]
 ATGTGTCCAACGGCAGCCTGA
 >seq id=12 start=695 stop=706 strand=+ frame=2 features=[]
-ATGCAACCCTGA</code></pre><p>This could also be done to writting a <code>FASTA</code> file with the nucleotide sequences of the ORFs using the <code>write_orfs_fna</code> function. Similarly for the <code>BED</code> and <code>GFF</code> files using the <code>write_orfs_bed</code> and <code>write_orfs_gff</code> functions respectively.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simplecodingrule/">« A Simple Coding Rule</a><a class="docs-footer-nextpage" href="../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 19:55">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ATGCAACCCTGA</code></pre><p>This could also be done to writting a <code>FASTA</code> file with the nucleotide sequences of the ORFs using the <code>write_orfs_fna</code> function. Similarly for the <code>BED</code> and <code>GFF</code> files using the <code>write_orfs_bed</code> and <code>write_orfs_gff</code> functions respectively.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../simplecodingrule/">« A Simple Coding Rule</a><a class="docs-footer-nextpage" href="../api/">API »</a><div class="flexbox-break"></div><p class="footer-message">Powered by <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> and the <a href="https://julialang.org/">Julia Programming Language</a>.</p></nav></div><div class="modal" id="documenter-settings"><div class="modal-background"></div><div class="modal-card"><header class="modal-card-head"><p class="modal-card-title">Settings</p><button class="delete"></button></header><section class="modal-card-body"><p><label class="label">Theme</label><div class="select"><select id="documenter-themepicker"><option value="auto">Automatic (OS)</option><option value="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option><option value="catppuccin-latte">catppuccin-latte</option><option value="catppuccin-frappe">catppuccin-frappe</option><option value="catppuccin-macchiato">catppuccin-macchiato</option><option value="catppuccin-mocha">catppuccin-mocha</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 1.5.0 on <span class="colophon-date" title="Monday 29 July 2024 20:05">Monday 29 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>