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pheno-ranker: - metacpan.org
<!DOCTYPE html> <html lang="en-US"> <head> <title>pheno-ranker: - metacpan.org</title> <link rel="preload" as="fetch" href="/account/login_status" crossorigin="anonymous" /> <link href="/assets/style-XFEQ536G.css" rel="stylesheet" type="text/css"> <script src="/assets/main-C7YQGD7K.js" type="module"></script> <link rel="alternate" type="application/rss+xml" title="Recent CPAN Uploads of Pheno-Ranker - MetaCPAN" href="/dist/Pheno-Ranker/releases.rss" /> <link rel="canonical" href="https://metacpan.org/dist/Pheno-Ranker/view/bin/pheno-ranker" /> <meta name="description" content="A module that performs semantic similarity in PXF/BFF data structures and beyond (JSON|YAML)" /> <meta name="viewport" content="width=device-width, initial-scale=1, maximum-scale=5"> <link rel="shortcut icon" href="/static/icons/favicon.ico"> <link rel="apple-touch-icon" sizes="152x152" href="/static/icons/apple-touch-icon.png"> <link rel="search" href="/static/opensearch.xml" 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</div> </div> </form> <li class="icon-slidepanel visible-xs visible-sm"> <button data-toggle="slidepanel" data-target=".slidepanel"> <span class="button-fa-icon"> <i class="fa fa-bars slidepanel-open"></i> <i class="fa fa-times slidepanel-close"></i> </span> </button> </li> <li class="dropdown login-dropdown show-logged-in"> <button type="button" class="dropdown-toggle" data-toggle="dropdown"> <i class="fa fa-user button-fa-icon logged-in-icon" aria-hidden="true"></i> <i class="fas fa-chevron-down"></i> </button> <ul class="dropdown-menu"> <li><a href="/account/identities">Identities</a></li> <li><a href="/account/profile">Profile</a></li> <li><a href="/account/favorite/list">Favorites</a></li> <li> <a href="#" type="button" class="logout-button"> Logout </a> </li> </ul> </li> <li class="dropdown login-dropdown show-logged-out"> <button type="button" class="dropdown-toggle" data-toggle="dropdown"> <i class="fa fa-user button-fa-icon avatar-placeholder" aria-hidden="true"></i> <i class="fas fa-chevron-down"></i> </button> <ul class="dropdown-menu"> <li> <a href="/login/github"> <i class="fab fa-github fa-fw"></i> GitHub </a> </li> <li> <a href="/login/twitter"> <i class="fab fa-twitter fa-fw"></i> Twitter </a> </li> <li> <a href="/login/google"> <i class="fab fa-google fa-fw"></i> Google </a> </li> </ul> </li> <li class="dropdown login-dropdown hide-logged-in hide-logged-out"> <button> <i class="fa fa-user button-fa-icon" aria-hidden="true"></i> </button> </li> </ul> </nav> <div class="page-content "> <div class="top-notify-banner"> </div> <nav class="sidebar"> <div class="slidepanel"> <ul class="nav-list "> <li class="nav-header no-margin-top"> <div class="ttip" data-toggle="tooltip" data-placement="bottom" title="The date that this version of Pheno-Ranker was released."> <span class="relatize">27 Nov 2024 15:21:23 UTC</span> </div> </li> <li> Distribution: <a href="/release/MRUEDA/Pheno-Ranker-1.00">Pheno-Ranker</a> </li> <li> <a data-keyboard-shortcut="g s" href="/release/MRUEDA/Pheno-Ranker-1.00/source/bin/pheno-ranker">Source</a> (<a href="/release/MRUEDA/Pheno-Ranker-1.00/source/bin/pheno-ranker?raw=1">raw</a>) </li> <li> <a data-keyboard-shortcut="g b" href="/release/MRUEDA/Pheno-Ranker-1.00/source/bin">Browse</a> (<a href="/release/MRUEDA/Pheno-Ranker-1.00/source/bin?raw=1">raw</a>) </li> <li> <a data-keyboard-shortcut="g c" href="/release/MRUEDA/Pheno-Ranker-1.00/changes">Changes</a> </li> <li> <a rel="noopener nofollow" class="nopopup" href="https://github.com/CNAG-Biomedical-Informatics/pheno-ranker">Homepage</a> </li> <li> <a class="nopopup" href="/release/MRUEDA/Pheno-Ranker-1.00/contribute">How to Contribute</a> </li> <li> <a rel="noopener nofollow" data-keyboard-shortcut="g r" href="https://github.com/CNAG-Biomedical-Informatics/pheno-ranker">Repository</a> </li> <li> <a rel="noopener nofollow" data-keyboard-shortcut="g i" href="https://github.com/CNAG-Biomedical-Informatics/pheno-ranker/issues">Issues</a> (0) </li> <li> <a rel="noopener nofollow" href="http://matrix.cpantesters.org/?dist=Pheno-Ranker+1.00" title="Matrix">Testers</a> </li> <li> <a rel="noopener nofollow" href="http://cpants.cpanauthors.org/release/MRUEDA/Pheno-Ranker-1.00">Kwalitee</a> </li> <li> <div class="ttip" data-toggle="tooltip" data-placement="bottom" title="The # people with an indexing permission on Pheno-Ranker who have released something to CPAN in the last 2 years (i.e. the # people likely able to release critical fixes in a timely manner)"> Bus factor: 1 </div> </li> <li> License: perl_5 </li> <li> Perl: v5.26.0 </li> <li class="nav-header">Activity</li> <li> <div class="activity-graph"> <img src="/dist/Pheno-Ranker/activity.svg?res=month" /> <div class="comment">24 month</div> </div> </li> <li class="nav-header">Tools</li> <li> <a itemprop="downloadUrl" href="https://cpan.metacpan.org/authors/id/M/MR/MRUEDA/Pheno-Ranker-1.00.tar.gz"> Download (<span itemprop="fileSize">2.26MB</span>)</a> </li> <li> <a href="https://explorer.metacpan.org/?url=%2Fmodule%2FMRUEDA%2FPheno-Ranker-1.00%2Fbin%2Fpheno-ranker"> MetaCPAN Explorer </a> </li> <li> <a href="/dist/Pheno-Ranker/permissions"> Permissions </a> </li> <li> <a href="/dist/Pheno-Ranker/releases.rss"> Subscribe to distribution </a> </li> <li> <button class="btn btn-link" data-toggle="modal" data-target="#metacpan_install-instructions-dialog"> Install Instructions </button> </li> <li> <form action="/search"> <input type="hidden" name="q" value="dist:Pheno-Ranker"> <input type="search" name="q" placeholder="Search distribution" class="form-control tool-bar-form"> <input type="submit" style="display: none"> </form> </li> <li> <form action="https://grep.metacpan.org/search"> <input type="hidden" name="qd" value="Pheno-Ranker"> <input type="hidden" name="source" value="metacpan"> <input type="search" name="q" placeholder="grep distribution" class="form-control tool-bar-form"> <input type="submit" style="display: none"> </form> </li> <li class="version-jump"> <select class="select-navigator form-control tool-bar-form"> <option disabled selected>Jump to version</option> <option value="/release/MRUEDA/Pheno-Ranker-1.05/view/bin/pheno-ranker" >1.05 (MRUEDA on 2025-02-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.04/view/bin/pheno-ranker" >1.04 (MRUEDA on 2025-02-11)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.03/view/bin/pheno-ranker" >1.03 (MRUEDA on 2025-02-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.02/view/bin/pheno-ranker" >1.02 (MRUEDA on 2025-02-03)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.01/view/bin/pheno-ranker" >1.01 (MRUEDA on 2025-01-16)</option> <option disabled value="/release/MRUEDA/Pheno-Ranker-1.00/view/bin/pheno-ranker" >1.00 (MRUEDA on 2024-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.12/view/bin/pheno-ranker" >0.12 (MRUEDA on 2024-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.11/view/bin/pheno-ranker" >0.11 (MRUEDA on 2024-09-29)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.10/view/bin/pheno-ranker" >0.10 (MRUEDA on 2024-08-07)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.09/view/bin/pheno-ranker" >0.09 (MRUEDA on 2024-05-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.08/view/bin/pheno-ranker" >0.08 (MRUEDA on 2024-04-24)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.07/view/bin/pheno-ranker" >0.07 (MRUEDA on 2024-04-22)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.06/view/bin/pheno-ranker" >0.06 (MRUEDA on 2024-04-06)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.05/view/bin/pheno-ranker" >0.05 (MRUEDA on 2024-03-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.04/view/bin/pheno-ranker" >0.04 (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.03_1/view/bin/pheno-ranker" >0.03_1 DEV (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.03/view/bin/pheno-ranker" >0.03 (MRUEDA on 2023-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.02/view/bin/pheno-ranker" >0.02 (MRUEDA on 2023-10-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01_2/view/bin/pheno-ranker" >0.01_2 DEV (MRUEDA on 2023-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01_1/view/bin/pheno-ranker" >0.01_1 DEV (MRUEDA on 2023-10-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01/view/bin/pheno-ranker" >0.01 (MRUEDA on 2023-10-16)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_4/view/bin/pheno-ranker" >0.00_4 DEV (MRUEDA on 2023-10-13)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_3/view/bin/pheno-ranker" >0.00_3 DEV (MRUEDA on 2023-10-12)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_2/view/bin/pheno-ranker" >0.00_2 DEV (MRUEDA on 2023-09-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_1/view/bin/pheno-ranker" >0.00_1 DEV (MRUEDA on 2023-09-23)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_0/view/bin/pheno-ranker" >0.00_0 DEV (MRUEDA on 2023-09-22)</option> </select> </li> <li class="version-diff"> <select class="select-navigator form-control tool-bar-form"> <option disabled selected>Diff with version</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.05/bin/pheno-ranker" >1.05 (MRUEDA on 2025-02-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.04/bin/pheno-ranker" >1.04 (MRUEDA on 2025-02-11)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.03/bin/pheno-ranker" >1.03 (MRUEDA on 2025-02-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.02/bin/pheno-ranker" >1.02 (MRUEDA on 2025-02-03)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.01/bin/pheno-ranker" >1.01 (MRUEDA on 2025-01-16)</option> <option disabled value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-1.00/bin/pheno-ranker" >1.00 (MRUEDA on 2024-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.12/bin/pheno-ranker" >0.12 (MRUEDA on 2024-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.11/bin/pheno-ranker" >0.11 (MRUEDA on 2024-09-29)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.10/bin/pheno-ranker" >0.10 (MRUEDA on 2024-08-07)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.09/bin/pheno-ranker" >0.09 (MRUEDA on 2024-05-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.08/bin/pheno-ranker" >0.08 (MRUEDA on 2024-04-24)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.07/bin/pheno-ranker" >0.07 (MRUEDA on 2024-04-22)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.06/bin/pheno-ranker" >0.06 (MRUEDA on 2024-04-06)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.05/bin/pheno-ranker" >0.05 (MRUEDA on 2024-03-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.04/bin/pheno-ranker" >0.04 (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.03_1/bin/pheno-ranker" >0.03_1 DEV (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.03/bin/pheno-ranker" >0.03 (MRUEDA on 2023-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.02/bin/pheno-ranker" >0.02 (MRUEDA on 2023-10-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.01_2/bin/pheno-ranker" >0.01_2 DEV (MRUEDA on 2023-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.01_1/bin/pheno-ranker" >0.01_1 DEV (MRUEDA on 2023-10-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.01/bin/pheno-ranker" >0.01 (MRUEDA on 2023-10-16)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.00_4/bin/pheno-ranker" >0.00_4 DEV (MRUEDA on 2023-10-13)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.00_3/bin/pheno-ranker" >0.00_3 DEV (MRUEDA on 2023-10-12)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.00_2/bin/pheno-ranker" >0.00_2 DEV (MRUEDA on 2023-09-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.00_1/bin/pheno-ranker" >0.00_1 DEV (MRUEDA on 2023-09-23)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.00/diff/MRUEDA/Pheno-Ranker-0.00_0/bin/pheno-ranker" >0.00_0 DEV (MRUEDA on 2023-09-22)</option> </select> </li> <li> <ul class="dependencies"> <li class="nav-header">Dependencies</li> <li><a href="/pod/Data::Fake" title="Data::Fake" class="ellipsis">Data::Fake</a></li> <li><a href="/pod/File::ShareDir::ProjectDistDir" title="File::ShareDir::ProjectDistDir" class="ellipsis">File::ShareDir::ProjectDistDir</a></li> <li><a href="/pod/Graph" title="Graph" class="ellipsis">Graph</a></li> <li><a href="/pod/Hash::Fold" title="Hash::Fold" class="ellipsis">Hash::Fold</a></li> <li><a href="/pod/JSON::Validator" title="JSON::Validator" class="ellipsis">JSON::Validator</a></li> <li><a href="/pod/JSON::XS" title="JSON::XS" class="ellipsis">JSON::XS</a></li> <li><a href="/pod/Math::CDF" title="Math::CDF" class="ellipsis">Math::CDF</a></li> <li><a href="/pod/Moo" title="Moo" class="ellipsis">Moo</a></li> <li><a href="/pod/Path::Tiny" title="Path::Tiny" class="ellipsis">Path::Tiny</a></li> <li><a href="/pod/Scalar::Util" title="Scalar::Util" class="ellipsis">Scalar::Util</a></li> <li><a href="/pod/Sort::Naturally" title="Sort::Naturally" class="ellipsis">Sort::Naturally</a></li> <li><a href="/pod/Statistics::Descriptive" title="Statistics::Descriptive" class="ellipsis">Statistics::Descriptive</a></li> <li><a href="/pod/Term::ANSIColor" title="Term::ANSIColor" class="ellipsis">Term::ANSIColor</a></li> <li><a href="/pod/Text::CSV_XS" title="Text::CSV_XS" class="ellipsis">Text::CSV_XS</a></li> <li><a href="/pod/Types::Standard" title="Types::Standard" class="ellipsis">Types::Standard</a></li> <li><a href="/pod/YAML::XS" title="YAML::XS" class="ellipsis">YAML::XS</a></li> <li> <hr> </li> <li> <a href="/module/pheno-ranker:/requires">Reverse dependencies</a> </li> <li> <a href="http://deps.cpantesters.org/?module=pheno-ranker%3A">CPAN Testers List</a> </li> <li> <a href="https://cpandeps.grinnz.com/?dist=Pheno-Ranker&dist_version=1.00">Dependency graph</a> </li> </ul> </li> <li class="nav-header">Permalinks</li> <li> <a href="/release/MRUEDA/Pheno-Ranker-1.00/view/bin/pheno-ranker">This version</a> </li> <li> <a href="/dist/Pheno-Ranker/view/bin/pheno-ranker">Latest version</a> </li> <li> </li> <li> </li> </ul> </div> </nav> <div class="content-navigation"> <div class="breadcrumbs"> <span> <a data-keyboard-shortcut="g a" rel="author" href="/author/MRUEDA" class="author-name">Manuel Rueda</a> </span> <span> / </span> <div class="release dist-release status-cpan maturity-released"> <span class="dropdown"><b class="caret"></b></span> <select class="select-navigator "> <option value="/release/MRUEDA/Pheno-Ranker-1.05/view/bin/pheno-ranker" >1.05 (MRUEDA on 2025-02-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.04/view/bin/pheno-ranker" >1.04 (MRUEDA on 2025-02-11)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.03/view/bin/pheno-ranker" >1.03 (MRUEDA on 2025-02-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.02/view/bin/pheno-ranker" >1.02 (MRUEDA on 2025-02-03)</option> <option value="/release/MRUEDA/Pheno-Ranker-1.01/view/bin/pheno-ranker" >1.01 (MRUEDA on 2025-01-16)</option> <option selected value="/release/MRUEDA/Pheno-Ranker-1.00/view/bin/pheno-ranker" >1.00 (MRUEDA on 2024-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.12/view/bin/pheno-ranker" >0.12 (MRUEDA on 2024-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.11/view/bin/pheno-ranker" >0.11 (MRUEDA on 2024-09-29)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.10/view/bin/pheno-ranker" >0.10 (MRUEDA on 2024-08-07)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.09/view/bin/pheno-ranker" >0.09 (MRUEDA on 2024-05-04)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.08/view/bin/pheno-ranker" >0.08 (MRUEDA on 2024-04-24)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.07/view/bin/pheno-ranker" >0.07 (MRUEDA on 2024-04-22)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.06/view/bin/pheno-ranker" >0.06 (MRUEDA on 2024-04-06)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.05/view/bin/pheno-ranker" >0.05 (MRUEDA on 2024-03-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.04/view/bin/pheno-ranker" >0.04 (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.03_1/view/bin/pheno-ranker" >0.03_1 DEV (MRUEDA on 2023-12-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.03/view/bin/pheno-ranker" >0.03 (MRUEDA on 2023-11-27)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.02/view/bin/pheno-ranker" >0.02 (MRUEDA on 2023-10-19)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01_2/view/bin/pheno-ranker" >0.01_2 DEV (MRUEDA on 2023-10-18)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01_1/view/bin/pheno-ranker" >0.01_1 DEV (MRUEDA on 2023-10-17)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.01/view/bin/pheno-ranker" >0.01 (MRUEDA on 2023-10-16)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_4/view/bin/pheno-ranker" >0.00_4 DEV (MRUEDA on 2023-10-13)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_3/view/bin/pheno-ranker" >0.00_3 DEV (MRUEDA on 2023-10-12)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_2/view/bin/pheno-ranker" >0.00_2 DEV (MRUEDA on 2023-09-26)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_1/view/bin/pheno-ranker" >0.00_1 DEV (MRUEDA on 2023-09-23)</option> <option value="/release/MRUEDA/Pheno-Ranker-0.00_0/view/bin/pheno-ranker" >0.00_0 DEV (MRUEDA on 2023-09-22)</option> </select> <a data-keyboard-shortcut="g d" class="release-name" href="/release/MRUEDA/Pheno-Ranker-1.00">Pheno-Ranker-1.00</a> </div> <a class="latest" href="/pod/pheno-ranker:" title="go to latest"><span class="fa fa-step-forward"></span></a> <span class="river-gauge-gauge"> <svg width="24px" height="15px" version="1.1" xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink"> <g> <title> River stage zero No dependents </title> <rect x="0" y="0" width="4" height="15" fill="#e4e2e2" /> <rect x="5" y="0" width="4" height="15" fill="#e4e2e2" /> <rect x="10" y="0" width="4" height="15" fill="#e4e2e2" /> <rect x="15" y="0" width="4" height="15" fill="#e4e2e2" /> <rect x="20" y="0" width="4" height="15" fill="#e4e2e2" /> </g> </svg> </span> <div id="Pheno-Ranker-fav" class="show-logged-in"> <form action="/account/favorite/add" style="display: inline" method="POST"> <input type="hidden" name="remove" value="0"> <input type="hidden" name="release" value="Pheno-Ranker-1.00"> <input type="hidden" name="author" value="MRUEDA"> <input type="hidden" name="distribution" value="Pheno-Ranker"> <button type="submit" class="favorite"><span></span> ++</button> </form> </div> <div class="show-logged-out"> <button class="fav-not-logged-in favorite"><span></span> ++</button> </div> / <span>pheno-ranker:</span> </div> </div> <main class="content"> <nav class="toc"> <div class="toc-header"><strong>Contents</strong></div> <ul> <li><a href="#NAME">NAME</a></li> <li><a href="#SYNOPSIS">SYNOPSIS</a></li> <li><a href="#DESCRIPTION">DESCRIPTION</a></li> <li><a href="#SUMMARY">SUMMARY</a></li> <li><a href="#INSTALLATION">INSTALLATION</a> <ul> <li><a href="#Non-containerized">Non containerized</a> <ul> <li><a href="#Method-1%3A-From-CPAN">Method 1: From CPAN</a></li> <li><a href="#Method-2%3A-From-CPAN-in-a-CONDA-environment">Method 2: From CPAN in a CONDA environment</a></li> <li><a href="#Method-3%3A-From-GitHub">Method 3: From GitHub</a></li> </ul> </li> <li><a href="#Containerized">Containerized</a> <ul> <li><a href="#Method-4%3A-From-Docker-Hub">Method 4: From Docker Hub</a></li> <li><a href="#Method-5%3A-With-Dockerfile">Method 5: With Dockerfile</a></li> <li><a href="#Additional-instructions-for-Methods-4-and-5">Additional instructions for Methods 4 and 5</a></li> <li><a href="#Mounting-volumes">Mounting volumes</a></li> <li><a href="#System-requirements">System requirements</a></li> </ul> </li> </ul> </li> <li><a href="#HOW-TO-RUN-PHENO-RANKER">HOW TO RUN PHENO-RANKER</a> <ul> <li><a href="#COMMON-ERRORS-AND-SOLUTIONS">COMMON ERRORS AND SOLUTIONS</a></li> </ul> </li> <li><a href="#CITATION">CITATION</a></li> <li><a href="#AUTHOR">AUTHOR</a></li> <li><a href="#COPYRIGHT-AND-LICENSE">COPYRIGHT AND LICENSE</a></li> </ul></nav> <div class="pod anchors"> <h1 id="NAME">NAME</h1> <p>pheno-ranker: A script that performs semantic similarity in PXF/BFF data structures and beyond (JSON|YAML)</p> <h1 id="SYNOPSIS">SYNOPSIS</h1> <pre><code>pheno-ranker -r <individuals.json> -t <patient.json> [-options] Arguments: * Cohort mode: -r, --reference <file> BFF/PXF file(s) in JSON or YAML format (array or object) * Patient mode: -t, --target <file> BFF/PXF file in JSON or YAML format (object or array of 1 object) Options: -age Include age-related variables; excludes agent-like terms (BFF/PXF-only) [>no-age|age] -a, --align [path/basename] Write alignment file(s). If not specified, default filenames are used [default: alignment.*] -append-prefixes <prefixes> Prefixes for primary_key when #cohorts >= 2 [default: C] -config <file> YAML config file to modify default parameters [default: share/conf/config.yaml] -cytoscape-json [file] Serializes the pairwise comparison matrix as an undirected graph in JSON, compatible with Cytoscape [default: graph.json] -e, --export [path/basename] Export miscellaneous JSON files. If not specified, default filenames are used [default: export.*] -exclude-terms <terms> Exclude BFF/PXF terms (e.g., --exclude-terms sex, id) or column names in JSON-derived from CSV -graph-stats [file] Generates a text file with key graph metrics, for use with <-cytoscape-json> [default: graph_stats.txt] -include-hpo-ascendants Include ascendant terms from the Human Phenotype Ontology (HPO) -include-terms <terms> Include BFF/PXF terms (e.g., --include-terms diseases) or column names in JSON-derived from CSV -max-number-var <number> Maximum variables for binary string [default: 10000] -max-out <number> Print only N comparisons [default: 50] -o, --out-file <file> Output file path [default: -r matrix.txt | -t rank.txt] -poi, --patients-of-interest <id_list> Export JSON files for the selected individual IDs during a dry-run -poi-out-dir <directory> Directory for JSON files (used with --poi) -similarity-metric-cohort <metric> Similarity metric for cohort mode [>hamming|jaccard] -sort-by <metric> Sort by Hamming distance or Jaccard index [>hamming|jaccard] -w, --weights <file> YAML file with weights Generic Options: -debug <level> Print debugging (from 1 to 5, being 5 max) -h, --help Brief help message -log Save log file [default: pheno-ranker-log.json] -man Full documentation -no-color Toggle color output [>color|no-color] -v, --verbose Verbosity on -V, --version Print version</code></pre> <h1 id="DESCRIPTION">DESCRIPTION</h1> <p>pheno-ranker: A script that performs semantic similarity in PXF/BFF data structures and beyond (JSON|YAML)</p> <p>The script also accepts CSV files that have been pre-processed using the <code>csv2pheno-ranker</code> utility (included).</p> <h1 id="SUMMARY">SUMMARY</h1> <p>Pheno-Ranker is a lightweight and easy to install tool specifically designed for performing semantic similarity analysis on phenotypic data structured in JSON format, such as Beacon v2 Models or Phenopackets v2.</p> <h1 id="INSTALLATION">INSTALLATION</h1> <h2 id="Non-containerized"><a id="Non"></a>Non containerized</h2> <p>The script runs on command-line Linux and it has been tested on Debian/RedHat/macOS based distributions (only showing commands for Debian). Perl 5 is installed by default on Linux, but we will install a few CPAN modules with <code>cpanminus</code>.</p> <h3 id="Method-1:-From-CPAN"><a id="Method"></a>Method 1: From CPAN</h3> <p>First install system level dependencies:</p> <pre><code>sudo apt-get install cpanminus libperl-dev</code></pre> <p>Now you have to choose between one of the 2 options below:</p> <p><b>Option 1:</b> System-level installation:</p> <pre><code>cpanm --notest --sudo Pheno::Ranker pheno-ranker -h</code></pre> <p><b>Option 2:</b> Install Pheno-Ranker and the dependencies at <code>~/perl5</code></p> <pre><code>cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) cpanm --notest Pheno::Ranker pheno-ranker --help</code></pre> <p>To ensure Perl recognizes your local modules every time you start a new terminal, you should type:</p> <pre><code>echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc</code></pre> <h3 id="Method-2:-From-CPAN-in-a-CONDA-environment"><a id="Method1"></a>Method 2: From CPAN in a CONDA environment</h3> <p>Please follow <a href="https://cnag-biomedical-informatics.github.io/pheno-ranker/download-and-installation/#__tabbed_1_2">these instructions</a>.</p> <h3 id="Method-3:-From-GitHub"><a id="Method2"></a>Method 3: From GitHub</h3> <pre><code>git clone https://github.com/cnag-biomedical-informatics/pheno-ranker.git cd pheno-ranker</code></pre> <p>Install system level dependencies:</p> <pre><code>sudo apt-get install cpanminus libperl-dev</code></pre> <p>Now you have to choose between one of the 2 options below:</p> <p><b>Option 1:</b> Install dependencies (they're harmless to your system) as <code>sudo</code>:</p> <pre><code>cpanm --notest --sudo --installdeps . bin/pheno-ranker --help </code></pre> <p><b>Option 2:</b> Install the dependencies at <code>~/perl5</code>:</p> <pre><code>cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib) cpanm --notest --installdeps . bin/pheno-ranker --help</code></pre> <p>To ensure Perl recognizes your local modules every time you start a new terminal, you should type:</p> <pre><code>echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bashrc</code></pre> <p><i>Optional:</i> If you want to use <code>utils/barcode</code> or <code>utils/bff_pxf_plot</code>:</p> <pre><code>sudo apt-get install python3-pip libzbar0 pip3 install -r requirements.txt</code></pre> <h2 id="Containerized">Containerized</h2> <h3 id="Method-4:-From-Docker-Hub"><a id="Method3"></a>Method 4: From Docker Hub</h3> <p>Download a docker image (latest version - amd64|x86-64) from <a href="https://hub.docker.com/r/manuelrueda/pheno-ranker">Docker Hub</a> by executing:</p> <pre><code>docker pull manuelrueda/pheno-ranker:latest docker image tag manuelrueda/pheno-ranker:latest cnag/pheno-ranker:latest</code></pre> <p>See additional instructions below.</p> <h3 id="Method-5:-With-Dockerfile"><a id="Method4"></a>Method 5: With Dockerfile</h3> <p>Please download the <code>Dockerfile</code> from the repo:</p> <pre><code>wget https://raw.githubusercontent.com/cnag-biomedical-informatics/pheno-ranker/main/Dockerfile</code></pre> <p>And then run:</p> <pre><code># Docker Version 19.03 and Above (Supports buildx) docker buildx build -t cnag/pheno-ranker:latest . # Docker Version Older than 19.03 (Does Not Support buildx) docker build -t cnag/pheno-ranker:latest .</code></pre> <h3 id="Additional-instructions-for-Methods-4-and-5"><a id="Additional"></a>Additional instructions for Methods 4 and 5</h3> <p>To run the container (detached) execute:</p> <pre><code>docker run -tid -e USERNAME=root --name pheno-ranker cnag/pheno-ranker:latest</code></pre> <p>To enter:</p> <pre><code>docker exec -ti pheno-ranker bash</code></pre> <p>The command-line executable can be found at:</p> <pre><code>/usr/share/pheno-ranker/bin/pheno-ranker</code></pre> <p>The default container user is <code>root</code> but you can also run the container as <code>$UID=1000</code> (<code>dockeruser</code>).</p> <pre><code> docker run --user 1000 -tid --name pheno-ranker cnag/pheno-ranker:latest</code></pre> <h3 id="Mounting-volumes"><a id="Mounting"></a>Mounting volumes</h3> <p>Docker containers are fully isolated. If you need the mount a volume to the container please use the following syntax (<code>-v host:container</code>). Find an example below (note that you need to change the paths to match yours):</p> <pre><code>docker run -tid --volume /media/mrueda/4TBT/data:/data --name pheno-ranker-mount cnag/pheno-ranker:latest</code></pre> <p>Then I will do something like this:</p> <pre><code># First I create an alias to simplify invocation (from the host) alias pheno-ranker='docker exec -ti pheno-ranker-mount /usr/share/pheno-ranker/bin/pheno-ranker' # Now I use the alias to run the command (note that I use the flag --o to specify the filepath) pheno-ranker -r /data/individuals.json -o /data/matrix.txt</code></pre> <h3 id="System-requirements"><a id="System"></a>System requirements</h3> <pre><code>* Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOS, OpenSUSE) should do as well. (It should also work on macOS and Windows Server, but we are only providing information for Linux here) * Perl 5 (>= 5.26 core; installed by default in most Linux distributions). Check the version with "perl -v". * >= 4GB of RAM * 1 core * At least 16GB HDD</code></pre> <h1 id="HOW-TO-RUN-PHENO-RANKER"><a id="HOW"></a>HOW TO RUN PHENO-RANKER</h1> <p>For executing pheno-ranker you will need a PXF/BFF file(s) in JSON|YAML format. The reference cohort must be a JSON array, where each individual data are consolidated in one object.</p> <p>You can download examples from <a href="https://github.com/CNAG-Biomedical-Informatics/pheno-ranker/tree/main/share/ex">this location</a>.</p> <p>There are two modes of operation:</p> <dl> <dt id="Cohort-mode:"><a id="Cohort"></a><a id="Cohort-mode"></a>Cohort mode:</dt> <dd> <p><b>Intra-cohort:</b> With <code>--r</code> argument and 1 cohort.</p> <p><b>Inter-cohort:</b> With <code>--r</code> and multiple cohort files. It can be used in combination with <code>--append-prefixes</code> to add prefixes to each individual id.</p> </dd> <dt id="Patient-Mode:"><a id="Patient"></a><a id="Patient-Mode"></a>Patient Mode:</dt> <dd> <p>With <code>-r</code> reference cohort(s) and <code>--t</code> patient data.</p> </dd> </dl> <p><b>Examples:</b></p> <pre><code>$ ./pheno-ranker -r phenopackets.json # intra-cohort $ ./pheno-ranker -r phenopackets.yaml -o my_matrix.txt # intra-cohort $ ./pheno-ranker -r phenopackets.json -w weights.yaml --exclude-terms sex ethnicity exposures # intra-cohort with weights $ $path/pheno-ranker -r individuals.json others.yaml --append-prefixes CANCER CONTROL # inter-cohort $ $path/pheno-ranker -r individuals.json -t patient.yaml -max-out 100 # mode patient</code></pre> <h2 id="COMMON-ERRORS-AND-SOLUTIONS"><a id="COMMON"></a>COMMON ERRORS AND SOLUTIONS</h2> <pre><code>* Error message: R plotting Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 1 did not have X elements Calls: as.matrix -> read.table -> scan Execution halted Solution: Make sure that the values of your primary key (e.g., "id") do not contain spaces (e.g., "my fav id" must be "my_fav_id") * Error message: Foo Solution: Bar</code></pre> <h1 id="CITATION">CITATION</h1> <p>The author requests that any published work that utilizes <code>Pheno-Ranker</code> includes a cite to the following reference:</p> <p>Leist, I.C. et al., (2024). Pheno-Ranker: a toolkit for comparison of phenotypic data stored in GA4GH standards and beyond. <i>BMC Bioinformatics</i>. DOI: 10.1186/s12859-024-05993-2</p> <h1 id="AUTHOR">AUTHOR</h1> <p>Written by Manuel Rueda, PhD. Info about CNAG can be found at <a href="https://www.cnag.eu">https://www.cnag.eu</a>.</p> <h1 id="COPYRIGHT-AND-LICENSE"><a id="COPYRIGHT"></a>COPYRIGHT AND LICENSE</h1> <p>This PERL file is copyrighted. 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