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<html lang="en"><head><meta charset="UTF-8"/><meta name="viewport" content="width=device-width, initial-scale=1.0"/><title>CLI Reference (WIP) · beefblup</title><script data-outdated-warner src="../assets/warner.js"></script><link rel="canonical" href="https://millironx.com/beefblup/beefblup-cli/"/><link href="https://cdnjs.cloudflare.com/ajax/libs/lato-font/3.0.0/css/lato-font.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/juliamono/0.039/juliamono-regular.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/fontawesome.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/solid.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.15.3/css/brands.min.css" rel="stylesheet" type="text/css"/><link href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.13.11/katex.min.css" rel="stylesheet" type="text/css"/><script>documenterBaseURL=".."</script><script src="https://cdnjs.cloudflare.com/ajax/libs/require.js/2.3.6/require.min.js" data-main="../assets/documenter.js"></script><script src="../siteinfo.js"></script><script src="../../versions.js"></script><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-dark.css" data-theme-name="documenter-dark" data-theme-primary-dark/><link class="docs-theme-link" rel="stylesheet" type="text/css" href="../assets/themes/documenter-light.css" data-theme-name="documenter-light" data-theme-primary/><script src="../assets/themeswap.js"></script></head><body><div id="documenter"><nav class="docs-sidebar"><div class="docs-package-name"><span class="docs-autofit"><a href="../">beefblup</a></span></div><form class="docs-search" action="../search/"><input class="docs-search-query" id="documenter-search-query" name="q" type="text" placeholder="Search docs"/></form><ul class="docs-menu"><li><a class="tocitem" href="../">Home</a></li><li><a class="tocitem" href="../how-to-calculate-epds/">How to Calculate EPDs</a></li><li class="is-active"><a class="tocitem" href>CLI Reference (WIP)</a><ul class="internal"><li><a class="tocitem" href="#Input-file"><span>Input file</span></a></li><li><a class="tocitem" href="#Synopsis"><span>Synopsis</span></a></li><li><a class="tocitem" href="#Command-line-basic-syntax"><span>Command line basic syntax</span></a></li><li><a class="tocitem" href="#Suppressing-automatically-calculated-fixed-effects"><span>Suppressing automatically-calculated fixed effects</span></a></li></ul></li></ul><div class="docs-version-selector field has-addons"><div class="control"><span class="docs-label button is-static is-size-7">Version</span></div><div class="docs-selector control is-expanded"><div class="select is-fullwidth is-size-7"><select id="documenter-version-selector"></select></div></div></div></nav><div class="docs-main"><header class="docs-navbar"><nav class="breadcrumb"><ul class="is-hidden-mobile"><li class="is-active"><a href>CLI Reference (WIP)</a></li></ul><ul class="is-hidden-tablet"><li class="is-active"><a href>CLI Reference (WIP)</a></li></ul></nav><div class="docs-right"><a class="docs-edit-link" href="https://github.com/MillironX/beefblup/blob/master/docs/src/beefblup-cli.md#" title="Edit on GitHub"><span class="docs-icon fab"></span><span class="docs-label is-hidden-touch">Edit on GitHub</span></a><a class="docs-settings-button fas fa-cog" id="documenter-settings-button" href="#" title="Settings"></a><a class="docs-sidebar-button fa fa-bars is-hidden-desktop" id="documenter-sidebar-button" href="#"></a></div></header><article class="content" id="documenter-page"><h1 id="beefblup-Command-Line-Interface-(CLI)-documentation"><a class="docs-heading-anchor" href="#beefblup-Command-Line-Interface-(CLI)-documentation">beefblup Command Line Interface (CLI) documentation</a><a id="beefblup-Command-Line-Interface-(CLI)-documentation-1"></a><a class="docs-heading-anchor-permalink" href="#beefblup-Command-Line-Interface-(CLI)-documentation" title="Permalink"></a></h1><blockquote><p><em>A work in progress</em></p></blockquote><p><strong>Notice:</strong> This document is a draft for what the command-line interface for beefblup would look like as of version 1.0, if beefblup was even a command-line application to begin with (it's not). It is modeled (loosely) after the man page format. It is not intended to be taken seriously, but instead to serve as a useful thought experiment and brainstorming ground on the future of beefblup. Please use it if it clarifies things for you. If it doesn't, ignore it.</p><h2 id="Input-file"><a class="docs-heading-anchor" href="#Input-file">Input file</a><a id="Input-file-1"></a><a class="docs-heading-anchor-permalink" href="#Input-file" title="Permalink"></a></h2><p>beefblup requires a very specific format of input file. The format may be in comma-separated values (CSV) or Excel 2007+ (XLSX) format. CSV files should not be quoted (and therefore cannot have commas within cell values). Other formats may be forthcoming.</p><p>A beefblup data file must have at least six columns appearing in this order:</p><ul><li>ID</li><li>Sire ID</li><li>Dam ID</li><li>Birthdate</li><li>Fixed effect(s)</li><li>Response variable(s)</li></ul><p>The first row always contains column names. The values of column names are unimportant for the first four columns, as they will always be treated the same regardless of the name. The generated report will use the column names of fixed effects and response variables as given.</p><p>Each fixed effect should have its own column, to as many as are needed. There is no limit to the number of fixed effects as defined by beefblup, however its dependencies might have some. The same rules apply to response variables.</p><p>Unknown values should be left blank (<code>,,</code>). Do not substitute null placeholders (e.g. <code>NULL</code>, <code>NA</code>, <code>0</code>, <code>nothing</code>, <code>undefined</code>, etc.) for unknown values.</p><p>An example spreadsheet might have the following format</p><table><tr><th style="text-align: right">ID</th><th style="text-align: right">Sire ID</th><th style="text-align: right">Dam ID</th><th style="text-align: right">Birthdate</th><th style="text-align: right">Sex</th><th style="text-align: right">Weaning Weight</th></tr><tr><td style="text-align: right">1</td><td style="text-align: right"></td><td style="text-align: right"></td><td style="text-align: right">1/1/1990</td><td style="text-align: right">Male</td><td style="text-align: right">354</td></tr><tr><td style="text-align: right">2</td><td style="text-align: right">1</td><td style="text-align: right"></td><td style="text-align: right">1/1/1990</td><td style="text-align: right">Female</td><td style="text-align: right">251</td></tr><tr><td style="text-align: right">3</td><td style="text-align: right">1</td><td style="text-align: right"></td><td style="text-align: right">1/1/1991</td><td style="text-align: right">Male</td><td style="text-align: right">327</td></tr><tr><td style="text-align: right">4</td><td style="text-align: right">1</td><td style="text-align: right">2</td><td style="text-align: right">1/1/1991</td><td style="text-align: right">Female</td><td style="text-align: right">328</td></tr><tr><td style="text-align: right">5</td><td style="text-align: right"></td><td style="text-align: right">2</td><td style="text-align: right">1/1/1991</td><td style="text-align: right">Male</td><td style="text-align: right">301</td></tr><tr><td style="text-align: right">6</td><td style="text-align: right"></td><td style="text-align: right"></td><td style="text-align: right">1/1/1991</td><td style="text-align: right">Female</td><td style="text-align: right">270</td></tr><tr><td style="text-align: right">7</td><td style="text-align: right"></td><td style="text-align: right"></td><td style="text-align: right">1/1/1992</td><td style="text-align: right">Male</td><td style="text-align: right">330</td></tr></table><h2 id="Synopsis"><a class="docs-heading-anchor" href="#Synopsis">Synopsis</a><a id="Synopsis-1"></a><a class="docs-heading-anchor-permalink" href="#Synopsis" title="Permalink"></a></h2><pre><code class="language-bash hljs">beefblup [-G SNPs_file] [-M num_response_vars] [-o report_spreadsheet]
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[--no-aod] [--no-year] [--no-season] [--no-autob] [--maternal] input_file
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[report_file]</code></pre><h2 id="Command-line-basic-syntax"><a class="docs-heading-anchor" href="#Command-line-basic-syntax">Command line basic syntax</a><a id="Command-line-basic-syntax-1"></a><a class="docs-heading-anchor-permalink" href="#Command-line-basic-syntax" title="Permalink"></a></h2><p>The most basic input is to simply pass the input file name to the program.</p><pre><code class="language-bash hljs">beefblup filename.csv</code></pre><p>In this case beefblup will insert fixed-effects for age-of-dam, year, and season, and will calculate the EBVs for the response variable in the final column. The report will then be saved as <code>filename_report.txt</code>.</p><h2 id="Suppressing-automatically-calculated-fixed-effects"><a class="docs-heading-anchor" href="#Suppressing-automatically-calculated-fixed-effects">Suppressing automatically-calculated fixed effects</a><a id="Suppressing-automatically-calculated-fixed-effects-1"></a><a class="docs-heading-anchor-permalink" href="#Suppressing-automatically-calculated-fixed-effects" title="Permalink"></a></h2><p>If you don't wish to include one of the automatically calculated fixed-effects from your model, you can pass arguments to suppress them.</p><h3 id="Suppress-Age-of-dam"><a class="docs-heading-anchor" href="#Suppress-Age-of-dam">Suppress Age-of-dam</a><a id="Suppress-Age-of-dam-1"></a><a class="docs-heading-anchor-permalink" href="#Suppress-Age-of-dam" title="Permalink"></a></h3><pre><code class="language-bash hljs">beefblup --no-aod filename.csv</code></pre><h3 id="Suppress-year"><a class="docs-heading-anchor" href="#Suppress-year">Suppress year</a><a id="Suppress-year-1"></a><a class="docs-heading-anchor-permalink" href="#Suppress-year" title="Permalink"></a></h3><pre><code class="language-bash hljs">beefblup --no-year filename.csv</code></pre><h3 id="Suppress-season"><a class="docs-heading-anchor" href="#Suppress-season">Suppress season</a><a id="Suppress-season-1"></a><a class="docs-heading-anchor-permalink" href="#Suppress-season" title="Permalink"></a></h3><pre><code class="language-bash hljs">beefblup --no-season filename.csv</code></pre><h3 id="Suppress-all-calculated-fixed-effects"><a class="docs-heading-anchor" href="#Suppress-all-calculated-fixed-effects">Suppress all calculated fixed effects</a><a id="Suppress-all-calculated-fixed-effects-1"></a><a class="docs-heading-anchor-permalink" href="#Suppress-all-calculated-fixed-effects" title="Permalink"></a></h3><pre><code class="language-bash hljs">beefblup --no-autob filename.csv</code></pre><p>The argument <code>--no-autob</code> comes from the nomenclature of assigning fixed-effects to the matrix <em>b</em> in Henderson's mixed-model equations.</p></article><nav class="docs-footer"><a class="docs-footer-prevpage" href="../how-to-calculate-epds/">« How to Calculate EPDs</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="documenter-light">documenter-light</option><option value="documenter-dark">documenter-dark</option></select></div></p><hr/><p>This document was generated with <a href="https://github.com/JuliaDocs/Documenter.jl">Documenter.jl</a> version 0.27.5 on <span class="colophon-date" title="Wednesday 1 September 2021 01:08">Wednesday 1 September 2021</span>. Using Julia version 1.5.4.</p></section><footer class="modal-card-foot"></footer></div></div></div></body></html>
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