build based on fe3c212

dev/.documenter-siteinfo.json

@@ -1 +1 @@
-{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-03T22:47:22","documenter_version":"1.5.0"}}
+{"documenter":{"julia_version":"1.10.4","generation_timestamp":"2024-07-03T23:05:36","documenter_version":"1.5.0"}}

dev/api/index.html

@@ -51,4 +51,4 @@
 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="Wednesday 3 July 2024 22:47">Wednesday 3 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="Wednesday 3 July 2024 23:05">Wednesday 3 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="Wednesday 3 July 2024 22:47">Wednesday 3 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="Wednesday 3 July 2024 23:05">Wednesday 3 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 score=0.0
 ATGTGTCCAACGGCAGCCTGA
 >seq id=12 start=695 stop=706 strand=+ frame=2 score=0.0
-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="Wednesday 3 July 2024 22:47">Wednesday 3 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="Wednesday 3 July 2024 23:05">Wednesday 3 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>

dev/naivefinder/index.html

@@ -57,4 +57,4 @@
  MSPHKAM*
  M*
  MCPTAA*
- MQP*</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../features/">Scoring 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="Wednesday 3 July 2024 22:47">Wednesday 3 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
+ MQP*</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« Home</a><a class="docs-footer-nextpage" href="../features/">Scoring 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="Wednesday 3 July 2024 23:05">Wednesday 3 July 2024</span>. Using Julia version 1.10.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>