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2 changes: 1 addition & 1 deletion dev/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-21T16:29:45","documenter_version":"1.8.0"}}
{"documenter":{"julia_version":"1.11.1","generation_timestamp":"2024-11-22T08:29:09","documenter_version":"1.8.0"}}
14 changes: 7 additions & 7 deletions dev/accessing/index.html
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2 changes: 1 addition & 1 deletion dev/examples/index.html
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end
write(w, chr)
end
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Filtering: the @genes macro</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 16:29">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../genes/">« Filtering: the @genes macro</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 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:29">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
2 changes: 1 addition & 1 deletion dev/genes/index.html
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@genes(chr, :locus_tag in d[$:category1])

gene = chr.genes[5]
@genes(chr, gene == $gene)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/9f30598d5832659a8ecc8d5ea5f9ba654828ad42/src/macro.jl#L68-L126">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../loci/">« Representing genomic loci</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 16:29">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
@genes(chr, gene == $gene)</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/f9aa89b14b638c7e877c37d5ec883cbb42af4e18/src/macro.jl#L68-L126">source</a></section></article></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../loci/">« Representing genomic loci</a><a class="docs-footer-nextpage" href="../examples/">Examples »</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 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:29">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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open(GenBank.Writer, &quot;updated.gbk&quot;) do w
write(w, chr)
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="io/">I/O »</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 16:29">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></article><nav class="docs-footer"><a class="docs-footer-nextpage" href="io/">I/O »</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 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:29">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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for record in record
print(record)
end
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/9f30598d5832659a8ecc8d5ea5f9ba654828ad42/src/GenBank/reader.jl#L7-L19">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="GenomicAnnotations.GFF.Reader" href="#GenomicAnnotations.GFF.Reader"><code>GenomicAnnotations.GFF.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Reader(input::IO)</code></pre><p>Create a data reader of the GFF3 file format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/9f30598d5832659a8ecc8d5ea5f9ba654828ad42/src/GFF/reader.jl#L7-L11">source</a></section></article><h2 id="Output"><a class="docs-heading-anchor" href="#Output">Output</a><a id="Output-1"></a><a class="docs-heading-anchor-permalink" href="#Output" title="Permalink"></a></h2><p>Annotations can be printed with GenBank formatting using <code>GenBank.Writer</code>, and as GFF3 with <code>GFF.Writer</code>. Headers are not automatically converted between formats; <code>GFF.Writer</code> only prints the header of the first <code>Record</code>, and only if it starts with a <code>#</code>, while <code>GenBank.Writer</code> prints a default header if the stored one starts with <code>#</code>.</p><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="GenomicAnnotations.GenBank.Writer" href="#GenomicAnnotations.GenBank.Writer"><code>GenomicAnnotations.GenBank.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GenBank.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GenBank file format.</p><pre><code class="language-julia hljs">open(GenBank.Writer, outfile) do writer
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/f9aa89b14b638c7e877c37d5ec883cbb42af4e18/src/GenBank/reader.jl#L7-L19">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="GenomicAnnotations.GFF.Reader" href="#GenomicAnnotations.GFF.Reader"><code>GenomicAnnotations.GFF.Reader</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Reader(input::IO)</code></pre><p>Create a data reader of the GFF3 file format.</p></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/f9aa89b14b638c7e877c37d5ec883cbb42af4e18/src/GFF/reader.jl#L7-L11">source</a></section></article><h2 id="Output"><a class="docs-heading-anchor" href="#Output">Output</a><a id="Output-1"></a><a class="docs-heading-anchor-permalink" href="#Output" title="Permalink"></a></h2><p>Annotations can be printed with GenBank formatting using <code>GenBank.Writer</code>, and as GFF3 with <code>GFF.Writer</code>. Headers are not automatically converted between formats; <code>GFF.Writer</code> only prints the header of the first <code>Record</code>, and only if it starts with a <code>#</code>, while <code>GenBank.Writer</code> prints a default header if the stored one starts with <code>#</code>.</p><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="GenomicAnnotations.GenBank.Writer" href="#GenomicAnnotations.GenBank.Writer"><code>GenomicAnnotations.GenBank.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GenBank.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GenBank file format.</p><pre><code class="language-julia hljs">open(GenBank.Writer, outfile) do writer
write(writer, genome)
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/9f30598d5832659a8ecc8d5ea5f9ba654828ad42/src/GenBank/writer.jl#L11-L20">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="GenomicAnnotations.GFF.Writer" href="#GenomicAnnotations.GFF.Writer"><code>GenomicAnnotations.GFF.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GFF file format.</p><pre><code class="language-julia hljs">open(GFF.Writer, outfile) do writer
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/f9aa89b14b638c7e877c37d5ec883cbb42af4e18/src/GenBank/writer.jl#L11-L20">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="GenomicAnnotations.GFF.Writer" href="#GenomicAnnotations.GFF.Writer"><code>GenomicAnnotations.GFF.Writer</code></a> — <span class="docstring-category">Type</span><span class="is-flex-grow-1 docstring-article-toggle-button" title="Collapse docstring"></span></header><section><div><pre><code class="language-julia hljs">GFF.Writer(output::IO; width=70)</code></pre><p>Create a data writer of the GFF file format.</p><pre><code class="language-julia hljs">open(GFF.Writer, outfile) do writer
write(writer, genome)
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/9f30598d5832659a8ecc8d5ea5f9ba654828ad42/src/GFF/writer.jl#L11-L20">source</a></section></article><p>In the REPL, instances of <code>Gene</code> are displayed as they would be in the annotation file.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« GenomicAnnotations.jl</a><a class="docs-footer-nextpage" href="../accessing/">Accessing and modifying annotations »</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 1.8.0 on <span class="colophon-date" title="Thursday 21 November 2024 16:29">Thursday 21 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
end</code></pre></div><a class="docs-sourcelink" target="_blank" href="https://github.com/BioJulia/GenomicAnnotations.jl/blob/f9aa89b14b638c7e877c37d5ec883cbb42af4e18/src/GFF/writer.jl#L11-L20">source</a></section></article><p>In the REPL, instances of <code>Gene</code> are displayed as they would be in the annotation file.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../">« GenomicAnnotations.jl</a><a class="docs-footer-nextpage" href="../accessing/">Accessing and modifying annotations »</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 1.8.0 on <span class="colophon-date" title="Friday 22 November 2024 08:29">Friday 22 November 2024</span>. Using Julia version 1.11.1.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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