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<h2 id="toc-title">Table of contents</h2>
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<li><a href="#obicount" id="toc-obicount" class="nav-link active" data-scroll-target="#obicount"><span class="toc-section-number">13.1</span> <code>obicount</code></a></li>
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<li><a href="#obidistribute" id="toc-obidistribute" class="nav-link" data-scroll-target="#obidistribute"><span class="toc-section-number">13.2</span> <code>obidistribute</code></a></li>
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<li><a href="#obifind" id="toc-obifind" class="nav-link" data-scroll-target="#obifind"><span class="toc-section-number">13.3</span> <code>obifind</code></a></li>
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<h1 class="title d-none d-lg-block"><span class="chapter-number">13</span> <span class="chapter-title">Utilities</span></h1>
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<h2 data-number="13.1" class="anchored" data-anchor-id="obicount"><span class="header-section-number">13.1</span> <code>obicount</code></h2>
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<p><code>obicount</code> counts the number of sequence records, the sum of the <code>count</code> attributes, and the sum of the length of all the sequences.</p>
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<p><em>Example:</em></p>
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<div class="sourceCode" id="cb1"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="ex">obicount</span> seq.fasta </span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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<p>Prints the number of sequence records contained in the <code>seq.fasta</code> file and the sum of their <code>count</code> attributes.</p>
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<p><em>Options specific to the command</em></p>
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<ul>
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<li><code>--reads|-r</code> Prints read counts.</li>
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<li><code>--symbols|-s</code> Prints symbol counts.</li>
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<li><code>--variants|-v</code> Prints variant counts.</li>
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let tooltip;
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if (window.bootstrap) {
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button.setAttribute("data-bs-toggle", "tooltip");
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button.setAttribute("data-bs-placement", "left");
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button.setAttribute("data-bs-title", "Copied!");
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tooltip = new bootstrap.Tooltip(button,
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{ trigger: "manual",
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customClass: "code-copy-button-tooltip",
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|
offset: [0, -8]});
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|
tooltip.show();
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|
}
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setTimeout(function() {
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|
if (tooltip) {
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tooltip.hide();
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button.removeAttribute("data-bs-title");
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button.removeAttribute("data-bs-toggle");
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button.removeAttribute("data-bs-placement");
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}
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button.setAttribute("title", currentTitle);
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button.classList.remove('code-copy-button-checked');
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}, 1000);
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// clear code selection
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e.clearSelection();
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});
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function tippyHover(el, contentFn) {
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|
const config = {
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|
allowHTML: true,
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content: contentFn,
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|
maxWidth: 500,
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|
delay: 100,
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|
arrow: false,
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appendTo: function(el) {
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|
return el.parentElement;
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},
|
|
interactive: true,
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interactiveBorder: 10,
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|
theme: 'quarto',
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placement: 'bottom-start'
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};
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window.tippy(el, config);
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}
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const noterefs = window.document.querySelectorAll('a[role="doc-noteref"]');
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for (var i=0; i<noterefs.length; i++) {
|
|
const ref = noterefs[i];
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tippyHover(ref, function() {
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|
// use id or data attribute instead here
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let href = ref.getAttribute('data-footnote-href') || ref.getAttribute('href');
|
|
try { href = new URL(href).hash; } catch {}
|
|
const id = href.replace(/^#\/?/, "");
|
|
const note = window.document.getElementById(id);
|
|
return note.innerHTML;
|
|
});
|
|
}
|
|
const findCites = (el) => {
|
|
const parentEl = el.parentElement;
|
|
if (parentEl) {
|
|
const cites = parentEl.dataset.cites;
|
|
if (cites) {
|
|
return {
|
|
el,
|
|
cites: cites.split(' ')
|
|
};
|
|
} else {
|
|
return findCites(el.parentElement)
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|
}
|
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} else {
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|
return undefined;
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}
|
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};
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var bibliorefs = window.document.querySelectorAll('a[role="doc-biblioref"]');
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for (var i=0; i<bibliorefs.length; i++) {
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const ref = bibliorefs[i];
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const citeInfo = findCites(ref);
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if (citeInfo) {
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tippyHover(citeInfo.el, function() {
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var popup = window.document.createElement('div');
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citeInfo.cites.forEach(function(cite) {
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var citeDiv = window.document.createElement('div');
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citeDiv.classList.add('hanging-indent');
|
|
citeDiv.classList.add('csl-entry');
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|
var biblioDiv = window.document.getElementById('ref-' + cite);
|
|
if (biblioDiv) {
|
|
citeDiv.innerHTML = biblioDiv.innerHTML;
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}
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|
popup.appendChild(citeDiv);
|
|
});
|
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return popup.innerHTML;
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});
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}
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}
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});
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</script>
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<a href="./library.html" class="pagination-link">
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<span class="nav-page-text">The GO <em>OBITools</em> library</span> <i class="bi bi-arrow-right-short"></i>
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