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nickjhathaway committed Oct 30, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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59 changes: 57 additions & 2 deletions References.html
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<a class="nav-link" href="./index.html">
<span class="menu-text">Home</span></a>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-format-info" role="link" data-bs-toggle="dropdown" aria-expanded="false">
<span class="menu-text">Format Info</span>
</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-format-info">
<li>
<a class="dropdown-item" href="./format/FormatOverview.html">
<span class="dropdown-text">PMO fields overview</span></a>
</li>
<li>
<a class="dropdown-item" href="./format/FormatExample.html">
<span class="dropdown-text">PMO Examples</span></a>
</li>
</ul>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-tools-installation" role="link" data-bs-toggle="dropdown" aria-expanded="false">
<span class="menu-text">Tools Installation</span>
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<span class="menu-text">pmotools-python usages</span>
</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-pmotools-python-usages">
<li>
<li class="dropdown-header"><span class="menuTitle">Command line interface</span></li>
<li><hr class="dropdown-divider"></li>
<li class="dropdown-header"><span class="menuTitle">pmotools-runner.py</span></li>
<li>
<a class="dropdown-item" href="./pmotools-python-usages/pmotools-runner.html">
<span class="dropdown-text">Command line interface to pmotools-python with pmotools-runner.py</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Extracting out of PMO</span></li>
<li>
<a class="dropdown-item" href="./pmotools-python-usages/extracting_allele_tables.html">
<span class="dropdown-text">Extracting allele tables using pmotools-python</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Subset PMO</span></li>
<li>
<a class="dropdown-item" href="./pmotools-python-usages/subsetting_from_PMO.html">
<span class="dropdown-text">Subsetting from a PMO using pmotools-python</span></a>
</li>
<li>
<a class="dropdown-item" href="./pmotools-python-usages/getting_basic_info_from_pmo.html">
<span class="dropdown-text">Getting basic info out of PMO using pmotools-python</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Handling Multiple PMOs</span></li>
<li>
<a class="dropdown-item" href="./pmotools-python-usages/handling_multiple_pmos.html">
<span class="dropdown-text">Handling multiple PMOs pmotools-python</span></a>
</li>
</ul>
</li>
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</header><div id="refs" class="references csl-bib-body hanging-indent" data-entry-spacing="0" role="list">
<div id="ref-Crystal-Ornelas2022-sk" class="csl-entry" role="listitem">
Crystal-Ornelas, Robert, Charuleka Varadharajan, Dylan O’Ryan, Kathleen Beilsmith, Benjamin Bond-Lamberty, Kristin Boye, Madison Burrus, et al. 2022. <span>“Enabling <span>FAIR</span> Data in Earth and Environmental Science with Community-Centric (Meta)data Reporting Formats.”</span> <em>Sci Data</em> 9 (1): 700.
</div>
<div id="ref-Oldoni2019-kb" class="csl-entry" role="listitem">
Oldoni, Fabio, Kenneth K Kidd, and Daniele Podini. 2019. <span>“Microhaplotypes in Forensic Genetics.”</span> <em>Forensic Sci. Int. Genet.</em> 38 (January): 54–69.
</div>
<div id="ref-noauthor_undated-jo" class="csl-entry" role="listitem">
<span>“<span>SRA</span> Metadata and Submission Overview.”</span> n.d. <a href="https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/" class="uri">https://www.ncbi.nlm.nih.gov/sra/docs/submitmeta/</a>.
</div>
<div id="ref-Tessema2022-fg" class="csl-entry" role="listitem">
Tessema, Sofonias K, Nicholas J Hathaway, Noam B Teyssier, Maxwell Murphy, Anna Chen, Ozkan Aydemir, Elias M Duarte, et al. 2022. <span>“Sensitive, Highly Multiplexed Sequencing of Microhaplotypes from the Plasmodium Falciparum Heterozygome.”</span> <em>J. Infect. Dis.</em> 225 (April): 1227–37.
</div>
<div id="ref-Vangay_Pajau2021-cd" class="csl-entry" role="listitem">
Vangay Pajau, Burgin Josephine, Johnston Anjanette, Beck Kristen L., Berrios Daniel C., Blumberg Kai, Canon Shane, et al. 2021. <span>“Microbiome Metadata Standards: Report of the National Microbiome Data Collaborative’s Workshop and <span>Follow-On</span> Activities.”</span> <em>mSystems</em> 6 (1): e01194–20.
</div>
<div id="ref-Weisenhorn2022-he" class="csl-entry" role="listitem">
Weisenhorn, Pamela, and Kathleen Beilsmith. 2022. <span>“<span>ESS-DIVE</span> Reporting Format for Amplicon Abundance Table.”</span> Environmental System Science Data Infrastructure for a Virtual Ecosystem; Environmental Systems Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE).
</div>
<div id="ref-Yilmaz2011-ao" class="csl-entry" role="listitem">
Yilmaz, Pelin, Renzo Kottmann, Dawn Field, Rob Knight, James R Cole, Linda Amaral-Zettler, Jack A Gilbert, et al. 2011. <span>“Minimum Information about a Marker Gene Sequence (<span>MIMARKS</span>) and Minimum Information about Any (x) Sequence (<span>MIxS</span>) Specifications.”</span> <em>Nat. Biotechnol.</em> 29 (5): 415–20.
</div>
</div>


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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/Portable_Microhaplotype_Object_Tools\/");
var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/PMO_Docs\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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41 changes: 39 additions & 2 deletions Tools_Installation/pmotools-python_installation.html
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<a class="nav-link" href="../index.html">
<span class="menu-text">Home</span></a>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-format-info" role="link" data-bs-toggle="dropdown" aria-expanded="false">
<span class="menu-text">Format Info</span>
</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-format-info">
<li>
<a class="dropdown-item" href="../format/FormatOverview.html">
<span class="dropdown-text">PMO fields overview</span></a>
</li>
<li>
<a class="dropdown-item" href="../format/FormatExample.html">
<span class="dropdown-text">PMO Examples</span></a>
</li>
</ul>
</li>
<li class="nav-item dropdown ">
<a class="nav-link dropdown-toggle" href="#" id="nav-menu-tools-installation" role="link" data-bs-toggle="dropdown" aria-expanded="false">
<span class="menu-text">Tools Installation</span>
Expand All @@ -132,9 +147,31 @@
<span class="menu-text">pmotools-python usages</span>
</a>
<ul class="dropdown-menu" aria-labelledby="nav-menu-pmotools-python-usages">
<li>
<li class="dropdown-header"><span class="menuTitle">Command line interface</span></li>
<li><hr class="dropdown-divider"></li>
<li class="dropdown-header"><span class="menuTitle">pmotools-runner.py</span></li>
<li>
<a class="dropdown-item" href="../pmotools-python-usages/pmotools-runner.html">
<span class="dropdown-text">Command line interface to pmotools-python with pmotools-runner.py</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Extracting out of PMO</span></li>
<li>
<a class="dropdown-item" href="../pmotools-python-usages/extracting_allele_tables.html">
<span class="dropdown-text">Extracting allele tables using pmotools-python</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Subset PMO</span></li>
<li>
<a class="dropdown-item" href="../pmotools-python-usages/subsetting_from_PMO.html">
<span class="dropdown-text">Subsetting from a PMO using pmotools-python</span></a>
</li>
<li>
<a class="dropdown-item" href="../pmotools-python-usages/getting_basic_info_from_pmo.html">
<span class="dropdown-text">Getting basic info out of PMO using pmotools-python</span></a>
</li>
<li class="dropdown-header"><span class="menuTitle">Handling Multiple PMOs</span></li>
<li>
<a class="dropdown-item" href="../pmotools-python-usages/handling_multiple_pmos.html">
<span class="dropdown-text">Handling multiple PMOs pmotools-python</span></a>
</li>
</ul>
</li>
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}
var localhostRegex = new RegExp(/^(?:http|https):\/\/localhost\:?[0-9]*\//);
var mailtoRegex = new RegExp(/^mailto:/);
var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/Portable_Microhaplotype_Object_Tools\/");
var filterRegex = new RegExp("https:\/\/PlasmoGenEpi\.github\.io\/PMO_Docs\/");
var isInternal = (href) => {
return filterRegex.test(href) || localhostRegex.test(href) || mailtoRegex.test(href);
}
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