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<section id="obijupyterhub---the-dna-metabarcoding-learning-server" class="level1">
<h1>OBIJupyterHub - the DNA Metabarcoding Learning Server</h1>
<section id="intended-use" class="level2">
<h2 class="anchored" data-anchor-id="intended-use">Intended use</h2>
<p>This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and <code>./start-jupyterhub.sh</code> takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at <code>http://localhost:8888</code>. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.</p>
</section>
<section id="prerequisites-with-quick-checks" class="level2">
<h2 class="anchored" data-anchor-id="prerequisites-with-quick-checks">Prerequisites (with quick checks)</h2>
<p>You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.</p>
<ul>
<li>macOS: install <a href="https://orbstack.dev/">OrbStack</a> (recommended) or Docker Desktop; both ship Docker Engine and Compose.</li>
<li>Linux: install Docker Engine and the Compose plugin from your distribution (e.g., <code>sudo apt install docker.io docker-compose-plugin</code>) or from Docker’s official packages.</li>
<li>Windows: install Docker Desktop with the WSL2 backend enabled.</li>
<li>Quarto CLI: get installers from <a href="https://quarto.org/docs/get-started/" class="uri">https://quarto.org/docs/get-started/</a>.</li>
<li>Python 3: any recent version is fine (only the standard library is used).</li>
</ul>
<p>Verify from a terminal; if a command is missing, install it before moving on:</p>
<div class="code-copy-outer-scaffold"><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">docker</span> <span class="at">--version</span></span>
<span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> compose version <span class="co"># or: docker-compose --version</span></span>
<span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="ex">quarto</span> <span class="at">--version</span></span>
<span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a><span class="ex">python3</span> <span class="at">--version</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="how-the-startup-script-works" class="level2">
<h2 class="anchored" data-anchor-id="how-the-startup-script-works">How the startup script works</h2>
<p><code>./start-jupyterhub.sh</code> is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:</p>
<ul>
<li>creates the <code>jupyterhub_volumes/</code> tree (caddy, course, shared, users, web…)</li>
<li>builds <code>jupyterhub-student</code> and <code>jupyterhub-hub</code> images</li>
<li>renders the Quarto site from <code>web_src/</code>, generates PDF galleries and <code>pages.json</code>, and copies everything into <code>jupyterhub_volumes/web/</code></li>
<li>runs <code>docker-compose up -d --remove-orphans</code></li>
</ul>
<p>You can tailor what it does with a few flags:</p>
<ul>
<li><code>--no-build</code> (or <code>--offline</code>): skip Docker image builds and reuse existing images (useful when offline).</li>
<li><code>--force-rebuild</code>: rebuild images without cache.</li>
<li><code>--stop-server</code>: stop the stack and remove student containers, then exit.</li>
<li><code>--update-lectures</code>: rebuild the course website only (no Docker stop/start).</li>
</ul>
</section>
<section id="installation-and-first-run" class="level2">
<h2 class="anchored" data-anchor-id="installation-and-first-run">Installation and first run</h2>
<ol type="1">
<li>Clone the project:</li>
</ol>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb2"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="fu">git</span> clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git</span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a><span class="bu">cd</span> OBIJupyterHub</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<ol start="2" type="1">
<li>(Optional) glance at the structure you’ll populate:</li>
</ol>
<pre><code>OBIJupyterHub
├── start-jupyterhub.sh - single entry point (build + render + start)
├── obijupyterhub - Docker images and stack definitions
│&nbsp;&nbsp; ├── docker-compose.yml
│&nbsp;&nbsp; ├── Dockerfile
│&nbsp;&nbsp; ├── Dockerfile.hub
│&nbsp;&nbsp; └── jupyterhub_config.py
├── jupyterhub_volumes - data persisted on the host
│&nbsp;&nbsp; ├── course - read-only for students (notebooks, data, bin, R packages)
│&nbsp;&nbsp; ├── shared - shared read/write space for everyone
│&nbsp;&nbsp; ├── users - per-user persistent data
│&nbsp;&nbsp; └── web - rendered course website
└── web_src - Quarto sources for the course website</code></pre>
<ol start="3" type="1">
<li>Prepare course materials (optional before first run):</li>
</ol>
<ul>
<li>Put notebooks, datasets, scripts, binaries, or PDFs for students under <code>jupyterhub_volumes/course/</code>. They will appear read-only at <code>/home/jovyan/work/course/</code>.</li>
<li>For collaborative work, drop files in <code>jupyterhub_volumes/shared/</code> (read/write for all at <code>/home/jovyan/work/shared/</code>).</li>
<li>Edit or add Quarto sources in <code>web_src/</code> to update the course website; the script will render them.</li>
</ul>
<ol start="4" type="1">
<li>Start everything (build + render + launch):</li>
</ol>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb4"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<ol start="5" type="1">
<li><p>Access JupyterHub in a browser at <code>http://localhost:8888</code>.</p></li>
<li><p>Stop the stack when you’re done (run from <code>obijupyterhub/</code>):</p></li>
</ol>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb5"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<section id="operating-the-stack-one-command-a-few-options" class="level3">
<h3 class="anchored" data-anchor-id="operating-the-stack-one-command-a-few-options">Operating the stack (one command, a few options)</h3>
<ul>
<li>Start or rebuild: <code>./start-jupyterhub.sh</code> (rebuilds images, regenerates the website, starts the stack).</li>
<li>Start without rebuilding images (offline): <code>./start-jupyterhub.sh --no-build</code></li>
<li>Force rebuild without cache: <code>./start-jupyterhub.sh --force-rebuild</code></li>
<li>Stop only: <code>./start-jupyterhub.sh --stop-server</code></li>
<li>Rebuild website only (no Docker stop/start): <code>./start-jupyterhub.sh --update-lectures</code></li>
<li>Access at <code>http://localhost:8888</code> (students: any username / password <code>metabar2025</code>; admin: <code>admin</code> / <code>admin2025</code>).</li>
<li>Check logs from <code>obijupyterhub/</code> with <code>docker-compose logs -f jupyterhub</code>.</li>
<li>Stop with <code>docker-compose down</code> (from <code>obijupyterhub/</code>). Rerun <code>./start-jupyterhub.sh</code> to start again or after config changes.</li>
</ul>
</section>
</section>
<section id="managing-shared-data" class="level2">
<h2 class="anchored" data-anchor-id="managing-shared-data">Managing shared data</h2>
<p>Each student lands in <code>/home/jovyan/work/</code> with three key areas: their own files, a shared space, and a read-only course space. Everything under <code>work/</code> is persisted on the host in <code>jupyterhub_volumes</code>.</p>
<pre><code>work/ # Personal workspace root (persistent)
├── [student files] # Their own files and notebooks
├── R_packages/ # Personal R packages (writable by student)
├── shared/ # Shared workspace (read/write, shared with all)
└── course/ # Course files (read-only, managed by admin)
├── R_packages/ # Shared R packages (read-only, installed by prof)
├── bin/ # Shared executables (in PATH)
└── [course materials] # Your course files</code></pre>
<p>R looks for packages in this order: personal <code>work/R_packages/</code>, then shared <code>work/course/R_packages/</code>, then system libraries. Because everything lives under <code>work/</code>, student files survive restarts.</p>
<section id="user-accounts" class="level3">
<h3 class="anchored" data-anchor-id="user-accounts">User Accounts</h3>
<p>Defaults are defined in <code>obijupyterhub/docker-compose.yml</code>: admin (<code>admin</code> / <code>admin2025</code>) with write access to <code>course/</code>, and students (any username, password <code>metabar2025</code>) with read-only access to <code>course/</code>. Adjust <code>JUPYTERHUB_ADMIN_PASSWORD</code> and <code>JUPYTERHUB_PASSWORD</code> there, then rerun <code>./start-jupyterhub.sh</code>.</p>
</section>
<section id="installing-r-packages-admin-only" class="level3">
<h3 class="anchored" data-anchor-id="installing-r-packages-admin-only">Installing R Packages (Admin Only)</h3>
<p>From the host, install shared R packages into <code>course/R_packages/</code>:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb7"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install packages</span></span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a><span class="ex">tools/install_packages.sh</span> reshape2 plotly knitr</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<p>Students can install their own packages into their personal <code>work/R_packages/</code>:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb8"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Install in personal library (each student has their own)</span></span>
<span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a><span class="fu">install.packages</span>(<span class="st">'mypackage'</span>) <span class="co"># Will install in work/R_packages/</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="using-r-packages-students" class="level3">
<h3 class="anchored" data-anchor-id="using-r-packages-students">Using R Packages (Students)</h3>
<p>Students simply load packages normally:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb9"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(reshape2) <span class="co"># R checks: 1) work/R_packages/ 2) work/course/R_packages/ 3) system</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="fu">library</span>(plotly)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<p>R automatically searches in this order:</p>
<ol type="1">
<li>Personal packages: <code>/home/jovyan/work/R_packages/</code> (R_LIBS_USER)</li>
<li>Prof packages: <code>/home/jovyan/work/course/R_packages/</code> (R_LIBS_SITE)</li>
<li>System packages</li>
</ol>
</section>
<section id="list-available-packages" class="level3">
<h3 class="anchored" data-anchor-id="list-available-packages">List Available Packages</h3>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb10"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="co"># List all available packages (personal + course + system)</span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a><span class="fu">installed.packages</span>()[,<span class="st">"Package"</span>]</span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-4"><a href="#cb10-4" aria-hidden="true" tabindex="-1"></a><span class="co"># Check personal packages</span></span>
<span id="cb10-5"><a href="#cb10-5" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/R_packages"</span>)</span>
<span id="cb10-6"><a href="#cb10-6" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb10-7"><a href="#cb10-7" aria-hidden="true" tabindex="-1"></a><span class="co"># Check course packages (installed by prof)</span></span>
<span id="cb10-8"><a href="#cb10-8" aria-hidden="true" tabindex="-1"></a><span class="fu">list.files</span>(<span class="st">"/home/jovyan/work/course/R_packages"</span>)</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="deposit-or-retrieve-course-and-student-files" class="level3">
<h3 class="anchored" data-anchor-id="deposit-or-retrieve-course-and-student-files">Deposit or retrieve course and student files</h3>
<p>On the host, place course files in <code>jupyterhub_volumes/course/</code> (they appear read-only to students), shared files in <code>jupyterhub_volumes/shared/</code>, and collect student work from <code>jupyterhub_volumes/users/</code>.</p>
</section>
</section>
<section id="user-management" class="level2">
<h2 class="anchored" data-anchor-id="user-management">User Management</h2>
<section id="option-1-predefined-user-list" class="level3">
<h3 class="anchored" data-anchor-id="option-1-predefined-user-list">Option 1: Predefined User List</h3>
<p>In <code>jupyterhub_config.py</code>, uncomment and modify:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb11"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allowed_users <span class="op">=</span> {<span class="st">'student1'</span>, <span class="st">'student2'</span>, <span class="st">'student3'</span>}</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
<section id="option-2-allow-everyone-for-testing" class="level3">
<h3 class="anchored" data-anchor-id="option-2-allow-everyone-for-testing">Option 2: Allow Everyone (for testing)</h3>
<p>By default, the configuration allows any user:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb12"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a>c.Authenticator.allow_all <span class="op">=</span> <span class="va">True</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<p>⚠️ <strong>Warning</strong>: DummyAuthenticator is ONLY for local testing!</p>
</section>
</section>
<section id="kernel-verification" class="level2">
<h2 class="anchored" data-anchor-id="kernel-verification">Kernel Verification</h2>
<p>Once logged in, create a new notebook and verify you have access to:</p>
<ul>
<li><strong>Python 3</strong> (default kernel)</li>
<li><strong>R</strong> (R kernel)</li>
<li><strong>Bash</strong> (bash kernel)</li>
</ul>
</section>
<section id="customization-for-your-labs" class="level2">
<h2 class="anchored" data-anchor-id="customization-for-your-labs">Customization for Your Labs</h2>
<section id="add-additional-r-packages" class="level3">
<h3 class="anchored" data-anchor-id="add-additional-r-packages">Add Additional R Packages</h3>
<p>Modify the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb13"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">R</span> <span class="at">-e</span> <span class="st">"install.packages(c('your_package'), repos='http://cran.rstudio.com/')"</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
</section>
<section id="add-python-packages" class="level3">
<h3 class="anchored" data-anchor-id="add-python-packages">Add Python Packages</h3>
<p>Add to the <code>Dockerfile</code> (before <code>USER ${NB_UID}</code>):</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb14"><pre class="sourceCode dockerfile code-with-copy"><code class="sourceCode dockerfile"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="kw">RUN</span> <span class="ex">pip</span> install numpy pandas matplotlib seaborn</span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
<p>Then rerun <code>./start-jupyterhub.sh</code> to rebuild and restart.</p>
</section>
<section id="change-port-if-8000-is-occupied" class="level3">
<h3 class="anchored" data-anchor-id="change-port-if-8000-is-occupied">Change Port (if 8000 is occupied)</h3>
<p>Modify in <code>docker-compose.yml</code>:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb15"><pre class="sourceCode yaml code-with-copy"><code class="sourceCode yaml"><span id="cb15-1"><a href="#cb15-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ports</span><span class="kw">:</span></span>
<span id="cb15-2"><a href="#cb15-2" aria-hidden="true" tabindex="-1"></a><span class="at"> </span><span class="kw">-</span><span class="at"> </span><span class="st">"8001:8000"</span><span class="co"> # Accessible on localhost:8001</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
</section>
<section id="advantages-of-this-approach" class="level2">
<h2 class="anchored" data-anchor-id="advantages-of-this-approach">Advantages of This Approach</h2>
<p>✅ <strong>Everything in Docker</strong>: No need to install Python/JupyterHub on your computer<br>
✅ <strong>Portable</strong>: Easy to deploy on another server<br>
✅ <strong>Isolated</strong>: No pollution of your system environment<br>
✅ <strong>Easy to Clean</strong>: A simple <code>docker-compose down</code> is enough<br>
✅ <strong>Reproducible</strong>: Students will have exactly the same environment</p>
</section>
<section id="troubleshooting" class="level2">
<h2 class="anchored" data-anchor-id="troubleshooting">Troubleshooting</h2>
<ul>
<li>Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify <code>/var/run/docker.sock</code> exists.</li>
<li>Student containers do not start: check <code>docker-compose logs jupyterhub</code> and confirm the images exist with <code>docker images | grep jupyterhub-student</code>.</li>
<li>Port conflict: change the published port in <code>docker-compose.yml</code>.</li>
</ul>
<p><strong>I want to start from scratch</strong>:</p>
<div class="code-copy-outer-scaffold"><div class="sourceCode" id="cb16"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb16-1"><a href="#cb16-1" aria-hidden="true" tabindex="-1"></a><span class="bu">pushd</span> obijupyterhub</span>
<span id="cb16-2"><a href="#cb16-2" aria-hidden="true" tabindex="-1"></a><span class="ex">docker-compose</span> down <span class="at">-v</span></span>
<span id="cb16-3"><a href="#cb16-3" aria-hidden="true" tabindex="-1"></a><span class="ex">docker</span> rmi jupyterhub-hub jupyterhub-student</span>
<span id="cb16-4"><a href="#cb16-4" aria-hidden="true" tabindex="-1"></a><span class="bu">popd</span></span>
<span id="cb16-5"><a href="#cb16-5" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb16-6"><a href="#cb16-6" aria-hidden="true" tabindex="-1"></a><span class="co"># Then rebuild everything</span></span>
<span id="cb16-7"><a href="#cb16-7" aria-hidden="true" tabindex="-1"></a><span class="ex">./start-jupyterhub.sh</span></span></code></pre></div><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></div>
</section>
</section>
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Readme.md
+199 -84
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@@ -1,106 +1,146 @@
# OBIJupyterHub - the DNA Metabarcoding Learning Server
# JupyterHub Configuration with OrbStack on Mac (all in Docker)
## Intended use
## Prerequisites
This project packages the MetabarcodingSchool training lab into one reproducible bundle. You get Python, R, and Bash kernels, a Quarto-built course website, and preconfigured admin/student accounts, so onboarding a class is a single command instead of a day of setup. Everything runs locally on a single machine, student work persists between sessions, and `./start-jupyterhub.sh` takes care of building images, rendering the site, preparing volumes, and bringing JupyterHub up at `http://localhost:8888`. Defaults (accounts, passwords, volumes) live in the repo so instructors can tweak them quickly.
You must have docker running on your computer
## Prerequisites (with quick checks)
- On MacOS, [OrbStack](https://orbstack.dev/ "A Docker implementation optimised for MacOS") is recommanded
You need Docker, Docker Compose, Quarto, and Python 3 available on the machine that will host the lab.
## Installation Steps
- macOS: install [OrbStack](https://orbstack.dev/) (recommended) or Docker Desktop; both ship Docker Engine and Compose.
- Linux: install Docker Engine and the Compose plugin from your distribution (e.g., `sudo apt install docker.io docker-compose-plugin`) or from Docker’s official packages.
- Windows: install Docker Desktop with the WSL2 backend enabled.
- Quarto CLI: get installers from <https://quarto.org/docs/get-started/>.
- Python 3: any recent version is fine (only the standard library is used).
Verify from a terminal; if a command is missing, install it before moving on:
```bash
docker --version
docker compose version # or: docker-compose --version
quarto --version
python3 --version
```
## How the startup script works
`./start-jupyterhub.sh` is the single entry point. It builds the Docker images, renders the course website, prepares the volume folders, and starts the stack. Internally it:
- creates the `jupyterhub_volumes/` tree (caddy, course, shared, users, web…)
- builds `jupyterhub-student` and `jupyterhub-hub` images
- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
- runs `docker-compose up -d --remove-orphans`
You can tailor what it does with a few flags:
- `--no-build` (or `--offline`): skip Docker image builds and reuse existing images (useful when offline).
- `--force-rebuild`: rebuild images without cache.
- `--stop-server`: stop the stack and remove student containers, then exit.
- `--update-lectures`: rebuild the course website only (no Docker stop/start).
- `--build-obidoc`: force rebuilding the obidoc documentation (auto-built if empty; skipped in offline mode).
## Installation and first run
1) Clone the project:
### 1. Create Directory Structure
```bash
git clone https://forge.metabarcoding.org/MetabarcodingSchool/OBIJupyterHub.git
```
Enter into the `OBIJupyterHub` directory
```bash
cd OBIJupyterHub
```
2) (Optional) glance at the structure you’ll populate:
#### File Structure
Your `OBIJupyterHub` directory should contain:
```
OBIJupyterHub
├── start-jupyterhub.sh - single entry point (build + render + start)
├── obijupyterhub - Docker images and stack definitions
├── start-jupyterhub.sh - The script used to setup and start the server
├── obijupyterhub - The files describing the docker images and the stack
│   ├── Caddyfile
│   ├── docker-compose.yml
│   ├── Dockerfile
│   ├── Dockerfile.hub
│   └── jupyterhub_config.py
├── jupyterhub_volumes - data persisted on the host
│   ├── course - read-only for students (notebooks, data, bin, R packages)
│   ├── shared - shared read/write space for everyone
│   ├── users - per-user persistent data
│   └── web - rendered course website
└── web_src - Quarto sources for the course website
│   ├── jupyterhub_config.py
│   ├── sftpgo_config.json
│   └── start-notebook.sh
├── jupyterhub_volumes - The directory containing the docker volumes
│   ├── caddy
│   ├── course - Read only volume mounted on every student container
│   │   ├── bin
│   │   └── R_packages
│   ├── jupyterhub
│   ├── shared - Read write volume shared in every student container
│   ├── users
│   └── web
│   ├── img
│   │   └── welcome_metabar.webp
│   ├── index.html
│   └── pages
├── Readme.md - This documentation
├── tools
│   ├── generate_pages_json.py
│   └── install_packages.sh
└─── web_src - The quarto document sources used to build the web site
   ├── _output
   ├── _quarto.yml
   ├── 00_home.qmd
   ├── lectures
   │   └── computers
   │   └── regex
   │   ├── lecture_regex.qmd
   │   ├── slides_regex.qmd
   │   └── slides.css
   └── scripts
   └── copy-to-web.sh
```
3) Prepare course materials (optional before first run):
- Put notebooks, datasets, scripts, binaries, or PDFs for students under `jupyterhub_volumes/course/`. They will appear read-only at `/home/jovyan/work/course/`.
- For collaborative work, drop files in `jupyterhub_volumes/shared/` (read/write for all at `/home/jovyan/work/shared/`).
- Edit or add Quarto sources in `web_src/` to update the course website; the script will render them.
### 2. Start JupyterHub
4) Start everything (build + render + launch):
From the terminal, in the `OBIJupyterHub` directory, run the following command:
```bash
``` bash
./start-jupyterhub.sh
```
5) Access JupyterHub in a browser at `http://localhost:8888`.
### 3. Access JupyterHub
6) Stop the stack when you’re done (run from `obijupyterhub/`):
Open your browser and go to: **http://localhost:8888**
```bash
You can log in as a student with any username and password: `metabar2025`
## Useful Commands
### View JupyterHub logs
``` bash
cd obijupyterhub
docker-compose logs -f jupyterhub
```
### View all containers (hub + students)
``` bash
docker ps | grep jupyterhub
```
### Stop JupyterHub
``` bash
cd obijupyterhub
docker-compose down
```
### Operating the stack (one command, a few options)
### Restart JupyterHub (after config modification)
- Start or rebuild: `./start-jupyterhub.sh` (rebuilds images, regenerates the website, starts the stack).
- Start without rebuilding images (offline): `./start-jupyterhub.sh --no-build`
- Force rebuild without cache: `./start-jupyterhub.sh --force-rebuild`
- Stop only: `./start-jupyterhub.sh --stop-server`
- Rebuild website only (no Docker stop/start): `./start-jupyterhub.sh --update-lectures`
- Rebuild obidoc docs: `./start-jupyterhub.sh --build-obidoc` (also builds automatically if `jupyterhub_volumes/web/obidoc` is empty; skipped in offline mode)
- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.
``` bash
cd obijupyterhub
docker-compose restart jupyterhub
```
## Managing shared data
### View logs for a specific student
Each student lands in `/home/jovyan/work/` with three key areas: their own files, a shared space, and a read-only course space. Everything under `work/` is persisted on the host in `jupyterhub_volumes`.
``` bash
docker logs jupyter-<username>
```
Replace `<username>` by the actual username of the student.
### Clean up after lab
``` bash
# Stop and remove all containers
cd obijupyterhub
docker-compose down
# Remove student containers
docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
# Remove volumes (WARNING: deletes student data)
docker volume ls | grep jupyterhub-user | awk '{print $2}' | xargs docker volume rm
# Clean everything (containers + volumes + network)
docker-compose down -v
docker ps -a | grep jupyter- | awk '{print $1}' | xargs docker rm -f
docker volume prune -f
```
## Managing Shared Data
### Directory Structure for Each Student
Each student will see this directory structure in their JupyterLab (everything under `work/` is persistent):
```
work/ # Personal workspace root (persistent)
@@ -113,22 +153,42 @@ work/ # Personal workspace root (persistent)
└── [course materials] # Your course files
```
R looks for packages in this order: personal `work/R_packages/`, then shared `work/course/R_packages/`, then system libraries. Because everything lives under `work/`, student files survive restarts.
**R Package Priority:**
1. R checks `work/R_packages/` first (personal, writable)
1. Then `work/course/R_packages/` (shared, read-only, installed by prof)
1. Then system libraries
**Important:** Everything is under `work/`, so all student files are automatically saved in their persistent volume.
### User Accounts
Defaults are defined in `obijupyterhub/docker-compose.yml`: admin (`admin` / `admin2025`) with write access to `course/`, and students (any username, password `metabar2025`) with read-only access to `course/`. Adjust `JUPYTERHUB_ADMIN_PASSWORD` and `JUPYTERHUB_PASSWORD` there, then rerun `./start-jupyterhub.sh`.
**Admin Account:**
- Username: `admin`
- Password: `admin2025` (change in docker-compose.yml: `JUPYTERHUB_ADMIN_PASSWORD`)
- Can write to `course/` directory
**Student Accounts:**
- Username: any name
- Password: `metabar2025` (change in docker-compose.yml: `JUPYTERHUB_PASSWORD`)
- Read-only access to `course/` directory
### Installing R Packages (Admin Only)
From the host, install shared R packages into `course/R_packages/`:
**From your Mac (recommended):**
``` bash
# Install packages
tools/install_packages.sh reshape2 plotly knitr
```
Students can install their own packages into their personal `work/R_packages/`:
This script: - Installs packages in the `course/R_packages/` directory - All students can use them (read-only) - No need to rebuild the image
**Students can also install their own packages:**
Students can install packages in their personal `work/R_packages/`:
```r
# Install in personal library (each student has their own)
@@ -163,9 +223,43 @@ list.files("/home/jovyan/work/R_packages")
list.files("/home/jovyan/work/course/R_packages")
```
### Deposit or retrieve course and student files
### Deposit Files for Course
On the host, place course files in `jupyterhub_volumes/course/` (they appear read-only to students), shared files in `jupyterhub_volumes/shared/`, and collect student work from `jupyterhub_volumes/users/`.
To put files in the `course/` directory (accessible read-only):
``` bash
# Create a temporary directory
mkdir -p ~/jupyterhub-tp/course-files
# Copy your files into it
cp my_notebooks.ipynb ~/jupyterhub-tp/course-files/
cp my_data.csv ~/jupyterhub-tp/course-files/
# Copy into Docker volume
docker run --rm \
-v jupyterhub-course:/target \
-v ~/jupyterhub-tp/course-files:/source \
alpine sh -c "cp -r /source/* /target/"
```
### Retrieve Student Work
``` bash
# List user volumes
docker volume ls | grep 'obijupyterhub_user-'
# Copy files from a specific student
docker run --rm \
-v obijupyterhub_user-alice:/source \
-v ~/submissions:/target \
alpine sh -c "cp -r /source/* /target/alice/"
# Copy all shared work
docker run --rm \
-v obijupyterhub_shared:/source \
-v ~/submissions/shared:/target \
alpine sh -c "cp -r /source/* /target/"
```
## User Management
@@ -205,7 +299,11 @@ Modify the `Dockerfile` (before `USER ${NB_UID}`):
RUN R -e "install.packages(c('your_package'), repos='http://cran.rstudio.com/')"
```
Then rerun `./start-jupyterhub.sh` to rebuild and restart.
Then restart the server (it rebuilds the images if needed):
```bash
./start-jupyterhub.sh
```
### Add Python Packages
@@ -215,7 +313,14 @@ Add to the `Dockerfile` (before `USER ${NB_UID}`):
RUN pip install numpy pandas matplotlib seaborn
```
Then rerun `./start-jupyterhub.sh` to rebuild and restart.
### Distribute Files to Students
Create a `files_lab/` directory and add to the `Dockerfile`:
``` dockerfile
COPY files_lab/ /home/${NB_USER}/lab/
RUN chown -R ${NB_UID}:${NB_GID} /home/${NB_USER}/lab
```
### Change Port (if 8000 is occupied)
@@ -236,19 +341,29 @@ ports:
## Troubleshooting
- Docker daemon unavailable: make sure OrbStack/Docker Desktop/daemon is running; verify `/var/run/docker.sock` exists.
- Student containers do not start: check `docker-compose logs jupyterhub` and confirm the images exist with `docker images | grep jupyterhub-student`.
- Port conflict: change the published port in `docker-compose.yml`.
**Error "Cannot connect to Docker daemon"**:
- Check that OrbStack is running
- Verify the socket exists: `ls -la /var/run/docker.sock`
**Student containers don't start**:
- Check logs: `docker-compose logs jupyterhub`
- Verify student image exists: `docker images | grep jupyterhub-student`
**Port 8000 already in use**:
- Change port in `docker-compose.yml`
**I want to start from scratch**:
``` bash
pushd obijupyterhub
push obijupyterhub
docker-compose down -v
docker rmi jupyterhub-hub jupyterhub-student
popd
# Then rebuild everything
./start-jupyterhub.sh
```
```
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* Bootstrap v5.3.1 (https://getbootstrap.com/)
* Copyright 2011-2023 The Bootstrap Authors
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
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rgb(109.8, 168, 253.8);--bs-secondary-tLine truncated
*
* ansi colors from IPython notebook's
*
* we also add `bright-[color]-` synonyms for the `-[color]-intense` classes since
* that seems to be what ansi_up emits
*
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* Bootstrap v5.3.1 (https://getbootstrap.com/)
* Copyright 2011-2023 The Bootstrap Authors (https://github.com/twbs/bootstrap/graphs/contributors)
* Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE)
*/
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//# sourceMappingURL=bootstrap.bundle.min.js.map
Readme_files/libs/clipboard/clipboard.min.js
Vendored
-7
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@@ -1,7 +0,0 @@
/*!
* clipboard.js v2.0.11
* https://clipboardjs.com/
*
* Licensed MIT © Zeno Rocha
*/
!function(t,e){"object"==typeof exports&&"object"==typeof module?module.exports=e():"function"==typeof define&&define.amd?define([],e):"object"==typeof exports?exports.ClipboardJS=e():t.ClipboardJS=e()}(this,function(){return n={686:function(t,e,n){"use strict";n.d(e,{default:function(){return b}});var e=n(279),i=n.n(e),e=n(370),u=n.n(e),e=n(817),r=n.n(e);function c(t){try{return document.execCommand(t)}catch(t){return}}var a=function(t){t=r()(t);return c("cut"),t};function o(t,e){var n,o,t=(n=t,o="rtl"===document.documentElement.getAttribute("dir"),(t=document.createElement("textarea")).style.fontSize="12pt",t.style.border="0",t.style.padding="0",t.style.margin="0",t.style.position="absolute",t.style[o?"right":"left"]="-9999px",o=window.pageYOffset||document.documentElement.scrollTop,t.style.top="".concat(o,"px"),t.setAttribute("readonly",""),t.value=n,t);return e.container.appendChild(t),e=r()(t),c("copy"),t.remove(),e}var f=function(t){var e=1<arguments.length&&void 0!==arguments[1]?arguments[1]:{container:document.body},n="";return"string"==typeof t?n=o(t,e):t instanceof HTMLInputElement&&!["text","search","url","tel","password"].includes(null==t?void 0:t.type)?n=o(t.value,e):(n=r()(t),c("copy")),n};function l(t){return(l="function"==typeof Symbol&&"symbol"==typeof Symbol.iterator?function(t){return typeof t}:function(t){return t&&"function"==typeof Symbol&&t.constructor===Symbol&&t!==Symbol.prototype?"symbol":typeof t})(t)}var s=function(){var t=0<arguments.length&&void 0!==arguments[0]?arguments[0]:{},e=t.action,n=void 0===e?"copy":e,o=t.container,e=t.target,t=t.text;if("copy"!==n&&"cut"!==n)throw new Error('Invalid "action" value, use either "copy" or "cut"');if(void 0!==e){if(!e||"object"!==l(e)||1!==e.nodeType)throw new Error('Invalid "target" value, use a valid Element');if("copy"===n&&e.hasAttribute("disabled"))throw new Error('Invalid "target" attribute. 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Readme_files/libs/quarto-html/anchor.min.js
Vendored
-9
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@@ -1,9 +0,0 @@
// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
//
// AnchorJS - v5.0.0 - 2023-01-18
// https://www.bryanbraun.com/anchorjs/
// Copyright (c) 2023 Bryan Braun; Licensed MIT
//
// @license magnet:?xt=urn:btih:d3d9a9a6595521f9666a5e94cc830dab83b65699&dn=expat.txt Expat
!function(A,e){"use strict";"function"==typeof define&&define.amd?define([],e):"object"==typeof module&&module.exports?module.exports=e():(A.AnchorJS=e(),A.anchors=new A.AnchorJS)}(globalThis,function(){"use strict";return function(A){function u(A){A.icon=Object.prototype.hasOwnProperty.call(A,"icon")?A.icon:"",A.visible=Object.prototype.hasOwnProperty.call(A,"visible")?A.visible:"hover",A.placement=Object.prototype.hasOwnProperty.call(A,"placement")?A.placement:"right",A.ariaLabel=Object.prototype.hasOwnProperty.call(A,"ariaLabel")?A.ariaLabel:"Anchor",A.class=Object.prototype.hasOwnProperty.call(A,"class")?A.class:"",A.base=Object.prototype.hasOwnProperty.call(A,"base")?A.base:"",A.truncate=Object.prototype.hasOwnProperty.call(A,"truncate")?Math.floor(A.truncate):64,A.titleText=Object.prototype.hasOwnProperty.call(A,"titleText")?A.titleText:""}function d(A){var e;if("string"==typeof A||A instanceof String)e=[].slice.call(document.querySelectorAll(A));else{if(!(Array.isArray(A)||A instanceof NodeList))throw new TypeError("The selector provided to AnchorJS was invalid.");e=[].slice.call(A)}return e}this.options=A||{},this.elements=[],u(this.options),this.add=function(A){var e,t,o,i,n,s,a,r,l,c,h,p=[];if(u(this.options),0!==(e=d(A=A||"h2, h3, h4, h5, h6")).length){for(null===document.head.querySelector("style.anchorjs")&&((A=document.createElement("style")).className="anchorjs",A.appendChild(document.createTextNode("")),void 0===(h=document.head.querySelector('[rel="stylesheet"],style'))?document.head.appendChild(A):document.head.insertBefore(A,h),A.sheet.insertRule(".anchorjs-link{opacity:0;text-decoration:none;-webkit-font-smoothing:antialiased;-moz-osx-font-smoothing:grayscale}",A.sheet.cssRules.length),A.sheet.insertRule(":hover>.anchorjs-link,.anchorjs-link:focus{opacity:1}",A.sheet.cssRules.length),A.sheet.insertRule("[data-anchorjs-icon]::after{content:attr(data-anchorjs-icon)}",A.sheet.cssRules.length),A.sheet.insertRule('@font-face{font-family:anchorjs-icons;src:url(data:n/a;base64,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) format("truetype")}',A.sheet.cssRules.length)),h=document.querySelectorAll("[id]"),t=[].map.call(h,function(A){return A.id}),i=0;i<e.length;i++)if(this.hasAnchorJSLink(e[i]))p.push(i);else{if(e[i].hasAttribute("id"))o=e[i].getAttribute("id");else if(e[i].hasAttribute("data-anchor-id"))o=e[i].getAttribute("data-anchor-id");else{for(r=a=this.urlify(e[i].textContent),s=0;n=t.indexOf(r=void 0!==n?a+"-"+s:r),s+=1,-1!==n;);n=void 0,t.push(r),e[i].setAttribute("id",r),o=r}(l=document.createElement("a")).className="anchorjs-link "+this.options.class,l.setAttribute("aria-label",this.options.ariaLabel),l.setAttribute("data-anchorjs-icon",this.options.icon),this.options.titleText&&(l.title=this.options.titleText),c=document.querySelector("base")?window.location.pathname+window.location.search:"",c=this.options.base||c,l.href=c+"#"+o,"always"===this.options.visible&&(l.style.opacity="1"),""===this.options.icon&&(l.style.font="1em/1 anchorjs-icons","left"===this.options.placement)&&(l.style.lineHeight="inherit"),"left"===this.options.placement?(l.style.position="absolute",l.style.marginLeft="-1.25em",l.style.paddingRight=".25em",l.style.paddingLeft=".25em",e[i].insertBefore(l,e[i].firstChild)):(l.style.marginLeft=".1875em",l.style.paddingRight=".1875em",l.style.paddingLeft=".1875em",e[i].appendChild(l))}for(i=0;i<p.length;i++)e.splice(p[i]-i,1);this.elements=this.elements.concat(e)}return this},this.remove=function(A){for(var e,t,o=d(A),i=0;i<o.length;i++)(t=o[i].querySelector(".anchorjs-link"))&&(-1!==(e=this.elements.indexOf(o[i]))&&this.elements.splice(e,1),o[i].removeChild(t));return this},this.removeAll=function(){thisLine truncated
// @license-end
Readme_files/libs/quarto-html/axe/axe-check.js
-145
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@@ -1,145 +0,0 @@
class QuartoAxeReporter {
constructor(axeResult, options) {
this.axeResult = axeResult;
this.options = options;
}
report() {
throw new Error("report() is an abstract method");
}
}
class QuartoAxeJsonReporter extends QuartoAxeReporter {
constructor(axeResult, options) {
super(axeResult, options);
}
report() {
console.log(JSON.stringify(this.axeResult, null, 2));
}
}
class QuartoAxeConsoleReporter extends QuartoAxeReporter {
constructor(axeResult, options) {
super(axeResult, options);
}
report() {
for (const violation of this.axeResult.violations) {
console.log(violation.description);
for (const node of violation.nodes) {
for (const target of node.target) {
console.log(target);
console.log(document.querySelector(target));
}
}
}
}
}
class QuartoAxeDocumentReporter extends QuartoAxeReporter {
constructor(axeResult, options) {
super(axeResult, options);
}
createViolationElement(violation) {
const violationElement = document.createElement("div");
const descriptionElement = document.createElement("div");
descriptionElement.className = "quarto-axe-violation-description";
descriptionElement.innerText = `${violation.impact.replace(/^[a-z]/, match => match.toLocaleUpperCase())}: ${violation.description}`;
violationElement.appendChild(descriptionElement);
const helpElement = document.createElement("div");
helpElement.className = "quarto-axe-violation-help";
helpElement.innerText = violation.help;
violationElement.appendChild(helpElement);
const nodesElement = document.createElement("div");
nodesElement.className = "quarto-axe-violation-nodes";
violationElement.appendChild(nodesElement);
const nodeElement = document.createElement("div");
nodeElement.className = "quarto-axe-violation-selector";
for (const node of violation.nodes) {
for (const target of node.target) {
const targetElement = document.createElement("span");
targetElement.className = "quarto-axe-violation-target";
targetElement.innerText = target;
nodeElement.appendChild(targetElement);
nodeElement.addEventListener("mouseenter", () => {
const element = document.querySelector(target);
if (element) {
element.scrollIntoView({ behavior: "smooth", block: "center" });
element.classList.add("quarto-axe-hover-highlight");
setTimeout(() => {
element.style.border = "";
}, 2000);
}
});
nodeElement.addEventListener("mouseleave", () => {
const element = document.querySelector(target);
if (element) {
element.classList.remove("quarto-axe-hover-highlight");
}
});
nodeElement.addEventListener("click", () => {
console.log(document.querySelector(target));
});
nodeElement.appendChild(targetElement);
}
nodesElement.appendChild(nodeElement);
}
return violationElement;
}
report() {
const violations = this.axeResult.violations;
const reportElement = document.createElement("div");
reportElement.className = "quarto-axe-report";
if (violations.length === 0) {
const noViolationsElement = document.createElement("div");
noViolationsElement.className = "quarto-axe-no-violations";
noViolationsElement.innerText = "No axe-core violations found.";
reportElement.appendChild(noViolationsElement);
}
violations.forEach((violation) => {
reportElement.appendChild(this.createViolationElement(violation));
});
document.querySelector("main").appendChild(reportElement);
}
}
const reporters = {
json: QuartoAxeJsonReporter,
console: QuartoAxeConsoleReporter,
document: QuartoAxeDocumentReporter,
};
class QuartoAxeChecker {
constructor(opts) {
this.options = opts;
}
async init() {
const axe = (await import("https://cdn.skypack.dev/pin/axe-core@v4.10.3-aVOFXWsJaCpVrtv89pCa/mode=imports,min/optimized/axe-core.js")).default;
const result = await axe.run({
exclude: [
// https://github.com/microsoft/tabster/issues/288
// MS has claimed they won't fix this, so we need to add an exclusion to
// all tabster elements
"[data-tabster-dummy]"
],
preload: { assets: ['cssom'], timeout: 50000 }
});
const reporter = this.options === true ? new QuartoAxeConsoleReporter(result) : new reporters[this.options.output](result, this.options);
reporter.report();
}
}
export async function init() {
const opts = document.querySelector("#quarto-axe-checker-options");
if (opts) {
const jsonOptions = JSON.parse(atob(opts.textContent));
const checker = new QuartoAxeChecker(jsonOptions);
await checker.init();
}
}
Readme_files/libs/quarto-html/popper.min.js
Vendored
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@@ -1,6 +0,0 @@
/**
* @popperjs/core v2.11.7 - MIT License
*/
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?t(exports):"function"==typeof define&&define.amd?define(["exports"],t):t((e="undefined"!=typeof globalThis?globalThis:e||self).Popper={})}(this,(function(e){"use strict";function t(e){if(null==e)return window;if("[object Window]"!==e.toString()){var t=e.ownerDocument;return t&&t.defaultView||window}return e}function n(e){return e instanceof t(e).Element||e instanceof Element}function r(e){return e instanceof t(e).HTMLElement||e instanceof HTMLElement}function o(e){return"undefined"!=typeof ShadowRoot&&(e instanceof t(e).ShadowRoot||e instanceof ShadowRoot)}var i=Math.max,a=Math.min,s=Math.round;function f(){var e=navigator.userAgentData;return null!=e&&e.brands&&Array.isArray(e.brands)?e.brands.map((function(e){return e.brand+"/"+e.version})).join(" "):navigator.userAgent}function c(){return!/^((?!chrome|android).)*safari/i.test(f())}function p(e,o,i){void 0===o&&(o=!1),void 0===i&&(i=!1);var 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j(e){return r(e)&&"fixed"!==m(e).position?e.offsetParent:null}function E(e){for(var n=t(e),i=j(e);i&&O(i)&&"static"===m(i).position;)i=j(i);return i&&("html"===l(i)||"body"===l(i)&&"static"===m(i).position)?n:i||function(e){var t=/firefox/i.test(f());if(/Trident/i.test(f())&&r(e)&&"fixed"===m(e).position)return null;var n=b(e);for(o(n)&&(n=n.host);r(n)&&["html","body"].indexOf(l(n))<0;){var i=m(n);if("none"!==i.transform||"none"!==i.perspective||"paint"===i.contain||-1!==["transform","perspective"].indexOf(i.willChange)||t&&"filter"===i.willChange||t&&i.filter&&"none"!==i.filter)return n;n=n.parentNode}return null}(e)||n}var D="top",A="bottom",L="right",P="left",M="auto",k=[D,A,L,P],W="start",B="end",H="viewport",T="popper",R=k.reduce((function(e,t){return e.concat([t+"-"+W,t+"-"+B])}),[]),S=[].concat(k,[M]).reduce((function(e,t){return e.concat([t,t+"-"+W,t+"-"+B])}),[]),V=["beforeRead","read","afterRead","beforeMain","main","afterMain","beforeWrite","write","afterWrite"];function 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Readme_files/libs/quarto-html/quarto-syntax-highlighting-587c61ba64f3a5504c4d52d930310e48.css
-236
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@@ -1,236 +0,0 @@
/* quarto syntax highlight colors */
:root {
--quarto-hl-ot-color: #003B4F;
--quarto-hl-at-color: #657422;
--quarto-hl-ss-color: #20794D;
--quarto-hl-an-color: #5E5E5E;
--quarto-hl-fu-color: #4758AB;
--quarto-hl-st-color: #20794D;
--quarto-hl-cf-color: #003B4F;
--quarto-hl-op-color: #5E5E5E;
--quarto-hl-er-color: #AD0000;
--quarto-hl-bn-color: #AD0000;
--quarto-hl-al-color: #AD0000;
--quarto-hl-va-color: #111111;
--quarto-hl-bu-color: inherit;
--quarto-hl-ex-color: inherit;
--quarto-hl-pp-color: #AD0000;
--quarto-hl-in-color: #5E5E5E;
--quarto-hl-vs-color: #20794D;
--quarto-hl-wa-color: #5E5E5E;
--quarto-hl-do-color: #5E5E5E;
--quarto-hl-im-color: #00769E;
--quarto-hl-ch-color: #20794D;
--quarto-hl-dt-color: #AD0000;
--quarto-hl-fl-color: #AD0000;
--quarto-hl-co-color: #5E5E5E;
--quarto-hl-cv-color: #5E5E5E;
--quarto-hl-cn-color: #8f5902;
--quarto-hl-sc-color: #5E5E5E;
--quarto-hl-dv-color: #AD0000;
--quarto-hl-kw-color: #003B4F;
}
/* other quarto variables */
:root {
--quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace;
}
/* syntax highlight based on Pandoc's rules */
pre > code.sourceCode > span {
color: #003B4F;
}
code.sourceCode > span {
color: #003B4F;
}
div.sourceCode,
div.sourceCode pre.sourceCode {
color: #003B4F;
}
/* Normal */
code span {
color: #003B4F;
}
/* Alert */
code span.al {
color: #AD0000;
font-style: inherit;
}
/* Annotation */
code span.an {
color: #5E5E5E;
font-style: inherit;
}
/* Attribute */
code span.at {
color: #657422;
font-style: inherit;
}
/* BaseN */
code span.bn {
color: #AD0000;
font-style: inherit;
}
/* BuiltIn */
code span.bu {
font-style: inherit;
}
/* ControlFlow */
code span.cf {
color: #003B4F;
font-weight: bold;
font-style: inherit;
}
/* Char */
code span.ch {
color: #20794D;
font-style: inherit;
}
/* Constant */
code span.cn {
color: #8f5902;
font-style: inherit;
}
/* Comment */
code span.co {
color: #5E5E5E;
font-style: inherit;
}
/* CommentVar */
code span.cv {
color: #5E5E5E;
font-style: italic;
}
/* Documentation */
code span.do {
color: #5E5E5E;
font-style: italic;
}
/* DataType */
code span.dt {
color: #AD0000;
font-style: inherit;
}
/* DecVal */
code span.dv {
color: #AD0000;
font-style: inherit;
}
/* Error */
code span.er {
color: #AD0000;
font-style: inherit;
}
/* Extension */
code span.ex {
font-style: inherit;
}
/* Float */
code span.fl {
color: #AD0000;
font-style: inherit;
}
/* Function */
code span.fu {
color: #4758AB;
font-style: inherit;
}
/* Import */
code span.im {
color: #00769E;
font-style: inherit;
}
/* Information */
code span.in {
color: #5E5E5E;
font-style: inherit;
}
/* Keyword */
code span.kw {
color: #003B4F;
font-weight: bold;
font-style: inherit;
}
/* Operator */
code span.op {
color: #5E5E5E;
font-style: inherit;
}
/* Other */
code span.ot {
color: #003B4F;
font-style: inherit;
}
/* Preprocessor */
code span.pp {
color: #AD0000;
font-style: inherit;
}
/* SpecialChar */
code span.sc {
color: #5E5E5E;
font-style: inherit;
}
/* SpecialString */
code span.ss {
color: #20794D;
font-style: inherit;
}
/* String */
code span.st {
color: #20794D;
font-style: inherit;
}
/* Variable */
code span.va {
color: #111111;
font-style: inherit;
}
/* VerbatimString */
code span.vs {
color: #20794D;
font-style: inherit;
}
/* Warning */
code span.wa {
color: #5E5E5E;
font-style: italic;
}
.prevent-inlining {
content: "</";
}
/*# sourceMappingURL=2dce1cc6c82594539e1579de68416b47.css.map */
Readme_files/libs/quarto-html/quarto.js
-847
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@@ -1,847 +0,0 @@
import * as tabsets from "./tabsets/tabsets.js";
import * as axe from "./axe/axe-check.js";
const sectionChanged = new CustomEvent("quarto-sectionChanged", {
detail: {},
bubbles: true,
cancelable: false,
composed: false,
});
const layoutMarginEls = () => {
// Find any conflicting margin elements and add margins to the
// top to prevent overlap
const marginChildren = window.document.querySelectorAll(
".column-margin.column-container > *, .margin-caption, .aside"
);
let lastBottom = 0;
for (const marginChild of marginChildren) {
if (marginChild.offsetParent !== null) {
// clear the top margin so we recompute it
marginChild.style.marginTop = null;
const top = marginChild.getBoundingClientRect().top + window.scrollY;
if (top < lastBottom) {
const marginChildStyle = window.getComputedStyle(marginChild);
const marginBottom = parseFloat(marginChildStyle["marginBottom"]);
const margin = lastBottom - top + marginBottom;
marginChild.style.marginTop = `${margin}px`;
}
const styles = window.getComputedStyle(marginChild);
const marginTop = parseFloat(styles["marginTop"]);
lastBottom = top + marginChild.getBoundingClientRect().height + marginTop;
}
}
};
window.document.addEventListener("DOMContentLoaded", function (_event) {
// Recompute the position of margin elements anytime the body size changes
if (window.ResizeObserver) {
const resizeObserver = new window.ResizeObserver(
throttle(() => {
layoutMarginEls();
if (
window.document.body.getBoundingClientRect().width < 990 &&
isReaderMode()
) {
quartoToggleReader();
}
}, 50)
);
resizeObserver.observe(window.document.body);
}
const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]');
const sidebarEl = window.document.getElementById("quarto-sidebar");
const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left");
const marginSidebarEl = window.document.getElementById(
"quarto-margin-sidebar"
);
// function to determine whether the element has a previous sibling that is active
const prevSiblingIsActiveLink = (el) => {
const sibling = el.previousElementSibling;
if (sibling && sibling.tagName === "A") {
return sibling.classList.contains("active");
} else {
return false;
}
};
// dispatch for htmlwidgets
// they use slideenter event to trigger resize
function fireSlideEnter() {
const event = window.document.createEvent("Event");
event.initEvent("slideenter", true, true);
window.document.dispatchEvent(event);
}
const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]');
tabs.forEach((tab) => {
tab.addEventListener("shown.bs.tab", fireSlideEnter);
});
// dispatch for shiny
// they use BS shown and hidden events to trigger rendering
function distpatchShinyEvents(previous, current) {
if (window.jQuery) {
if (previous) {
window.jQuery(previous).trigger("hidden");
}
if (current) {
window.jQuery(current).trigger("shown");
}
}
}
// tabby.js listener: Trigger event for htmlwidget and shiny
document.addEventListener(
"tabby",
function (event) {
fireSlideEnter();
distpatchShinyEvents(event.detail.previousTab, event.detail.tab);
},
false
);
// Track scrolling and mark TOC links as active
// get table of contents and sidebar (bail if we don't have at least one)
const tocLinks = tocEl
? [...tocEl.querySelectorAll("a[data-scroll-target]")]
: [];
const makeActive = (link) => tocLinks[link].classList.add("active");
const removeActive = (link) => tocLinks[link].classList.remove("active");
const removeAllActive = () =>
[...Array(tocLinks.length).keys()].forEach((link) => removeActive(link));
// activate the anchor for a section associated with this TOC entry
tocLinks.forEach((link) => {
link.addEventListener("click", () => {
if (link.href.indexOf("#") !== -1) {
const anchor = link.href.split("#")[1];
const heading = window.document.querySelector(
`[data-anchor-id="${anchor}"]`
);
if (heading) {
// Add the class
heading.classList.add("reveal-anchorjs-link");
// function to show the anchor
const handleMouseout = () => {
heading.classList.remove("reveal-anchorjs-link");
heading.removeEventListener("mouseout", handleMouseout);
};
// add a function to clear the anchor when the user mouses out of it
heading.addEventListener("mouseout", handleMouseout);
}
}
});
});
const sections = tocLinks.map((link) => {
const target = link.getAttribute("data-scroll-target");
if (target.startsWith("#")) {
return window.document.getElementById(decodeURI(`${target.slice(1)}`));
} else {
return window.document.querySelector(decodeURI(`${target}`));
}
});
const sectionMargin = 200;
let currentActive = 0;
// track whether we've initialized state the first time
let init = false;
const updateActiveLink = () => {
// The index from bottom to top (e.g. reversed list)
let sectionIndex = -1;
if (
window.innerHeight + window.pageYOffset >=
window.document.body.offsetHeight
) {
// This is the no-scroll case where last section should be the active one
sectionIndex = 0;
} else {
// This finds the last section visible on screen that should be made active
sectionIndex = [...sections].reverse().findIndex((section) => {
if (section) {
return window.pageYOffset >= section.offsetTop - sectionMargin;
} else {
return false;
}
});
}
if (sectionIndex > -1) {
const current = sections.length - sectionIndex - 1;
if (current !== currentActive) {
removeAllActive();
currentActive = current;
makeActive(current);
if (init) {
window.dispatchEvent(sectionChanged);
}
init = true;
}
}
};
const inHiddenRegion = (top, bottom, hiddenRegions) => {
for (const region of hiddenRegions) {
if (top <= region.bottom && bottom >= region.top) {
return true;
}
}
return false;
};
const categorySelector = "header.quarto-title-block .quarto-category";
const activateCategories = (href) => {
// Find any categories
// Surround them with a link pointing back to:
// #category=Authoring
try {
const categoryEls = window.document.querySelectorAll(categorySelector);
for (const categoryEl of categoryEls) {
const categoryText = categoryEl.textContent;
if (categoryText) {
const link = `${href}#category=${encodeURIComponent(categoryText)}`;
const linkEl = window.document.createElement("a");
linkEl.setAttribute("href", link);
for (const child of categoryEl.childNodes) {
linkEl.append(child);
}
categoryEl.appendChild(linkEl);
}
}
} catch {
// Ignore errors
}
};
function hasTitleCategories() {
return window.document.querySelector(categorySelector) !== null;
}
function offsetRelativeUrl(url) {
const offset = getMeta("quarto:offset");
return offset ? offset + url : url;
}
function offsetAbsoluteUrl(url) {
const offset = getMeta("quarto:offset");
const baseUrl = new URL(offset, window.location);
const projRelativeUrl = url.replace(baseUrl, "");
if (projRelativeUrl.startsWith("/")) {
return projRelativeUrl;
} else {
return "/" + projRelativeUrl;
}
}
// read a meta tag value
function getMeta(metaName) {
const metas = window.document.getElementsByTagName("meta");
for (let i = 0; i < metas.length; i++) {
if (metas[i].getAttribute("name") === metaName) {
return metas[i].getAttribute("content");
}
}
return "";
}
async function findAndActivateCategories() {
// Categories search with listing only use path without query
const currentPagePath = offsetAbsoluteUrl(
window.location.origin + window.location.pathname
);
const response = await fetch(offsetRelativeUrl("listings.json"));
if (response.status == 200) {
return response.json().then(function (listingPaths) {
const listingHrefs = [];
for (const listingPath of listingPaths) {
const pathWithoutLeadingSlash = listingPath.listing.substring(1);
for (const item of listingPath.items) {
const encodedItem = encodeURI(item);
if (
encodedItem === currentPagePath ||
encodedItem === currentPagePath + "index.html"
) {
// Resolve this path against the offset to be sure
// we already are using the correct path to the listing
// (this adjusts the listing urls to be rooted against
// whatever root the page is actually running against)
const relative = offsetRelativeUrl(pathWithoutLeadingSlash);
const baseUrl = window.location;
const resolvedPath = new URL(relative, baseUrl);
listingHrefs.push(resolvedPath.pathname);
break;
}
}
}
// Look up the tree for a nearby linting and use that if we find one
const nearestListing = findNearestParentListing(
offsetAbsoluteUrl(window.location.pathname),
listingHrefs
);
if (nearestListing) {
activateCategories(nearestListing);
} else {
// See if the referrer is a listing page for this item
const referredRelativePath = offsetAbsoluteUrl(document.referrer);
const referrerListing = listingHrefs.find((listingHref) => {
const isListingReferrer =
listingHref === referredRelativePath ||
listingHref === referredRelativePath + "index.html";
return isListingReferrer;
});
if (referrerListing) {
// Try to use the referrer if possible
activateCategories(referrerListing);
} else if (listingHrefs.length > 0) {
// Otherwise, just fall back to the first listing
activateCategories(listingHrefs[0]);
}
}
});
}
}
if (hasTitleCategories()) {
findAndActivateCategories();
}
const findNearestParentListing = (href, listingHrefs) => {
if (!href || !listingHrefs) {
return undefined;
}
// Look up the tree for a nearby linting and use that if we find one
const relativeParts = href.substring(1).split("/");
while (relativeParts.length > 0) {
const path = relativeParts.join("/");
for (const listingHref of listingHrefs) {
if (listingHref.startsWith(path)) {
return listingHref;
}
}
relativeParts.pop();
}
return undefined;
};
const manageSidebarVisiblity = (el, placeholderDescriptor) => {
let isVisible = true;
let elRect;
return (hiddenRegions) => {
if (el === null) {
return;
}
// Find the last element of the TOC
const lastChildEl = el.lastElementChild;
if (lastChildEl) {
// Converts the sidebar to a menu
const convertToMenu = () => {
for (const child of el.children) {
child.style.opacity = 0;
child.style.overflow = "hidden";
child.style.pointerEvents = "none";
}
nexttick(() => {
const toggleContainer = window.document.createElement("div");
toggleContainer.style.width = "100%";
toggleContainer.classList.add("zindex-over-content");
toggleContainer.classList.add("quarto-sidebar-toggle");
toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom
toggleContainer.id = placeholderDescriptor.id;
toggleContainer.style.position = "fixed";
const toggleIcon = window.document.createElement("i");
toggleIcon.classList.add("quarto-sidebar-toggle-icon");
toggleIcon.classList.add("bi");
toggleIcon.classList.add("bi-caret-down-fill");
const toggleTitle = window.document.createElement("div");
const titleEl = window.document.body.querySelector(
placeholderDescriptor.titleSelector
);
if (titleEl) {
toggleTitle.append(
titleEl.textContent || titleEl.innerText,
toggleIcon
);
}
toggleTitle.classList.add("zindex-over-content");
toggleTitle.classList.add("quarto-sidebar-toggle-title");
toggleContainer.append(toggleTitle);
const toggleContents = window.document.createElement("div");
toggleContents.classList = el.classList;
toggleContents.classList.add("zindex-over-content");
toggleContents.classList.add("quarto-sidebar-toggle-contents");
for (const child of el.children) {
if (child.id === "toc-title") {
continue;
}
const clone = child.cloneNode(true);
clone.style.opacity = 1;
clone.style.pointerEvents = null;
clone.style.display = null;
toggleContents.append(clone);
}
toggleContents.style.height = "0px";
const positionToggle = () => {
// position the element (top left of parent, same width as parent)
if (!elRect) {
elRect = el.getBoundingClientRect();
}
toggleContainer.style.left = `${elRect.left}px`;
toggleContainer.style.top = `${elRect.top}px`;
toggleContainer.style.width = `${elRect.width}px`;
};
positionToggle();
toggleContainer.append(toggleContents);
el.parentElement.prepend(toggleContainer);
// Process clicks
let tocShowing = false;
// Allow the caller to control whether this is dismissed
// when it is clicked (e.g. sidebar navigation supports
// opening and closing the nav tree, so don't dismiss on click)
const clickEl = placeholderDescriptor.dismissOnClick
? toggleContainer
: toggleTitle;
const closeToggle = () => {
if (tocShowing) {
toggleContainer.classList.remove("expanded");
toggleContents.style.height = "0px";
tocShowing = false;
}
};
// Get rid of any expanded toggle if the user scrolls
window.document.addEventListener(
"scroll",
throttle(() => {
closeToggle();
}, 50)
);
// Handle positioning of the toggle
window.addEventListener(
"resize",
throttle(() => {
elRect = undefined;
positionToggle();
}, 50)
);
window.addEventListener("quarto-hrChanged", () => {
elRect = undefined;
});
// Process the click
clickEl.onclick = () => {
if (!tocShowing) {
toggleContainer.classList.add("expanded");
toggleContents.style.height = null;
tocShowing = true;
} else {
closeToggle();
}
};
});
};
// Converts a sidebar from a menu back to a sidebar
const convertToSidebar = () => {
for (const child of el.children) {
child.style.opacity = 1;
child.style.overflow = null;
child.style.pointerEvents = null;
}
const placeholderEl = window.document.getElementById(
placeholderDescriptor.id
);
if (placeholderEl) {
placeholderEl.remove();
}
el.classList.remove("rollup");
};
if (isReaderMode()) {
convertToMenu();
isVisible = false;
} else {
// Find the top and bottom o the element that is being managed
const elTop = el.offsetTop;
const elBottom =
elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight;
if (!isVisible) {
// If the element is current not visible reveal if there are
// no conflicts with overlay regions
if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) {
convertToSidebar();
isVisible = true;
}
} else {
// If the element is visible, hide it if it conflicts with overlay regions
// and insert a placeholder toggle (or if we're in reader mode)
if (inHiddenRegion(elTop, elBottom, hiddenRegions)) {
convertToMenu();
isVisible = false;
}
}
}
}
};
};
const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]');
for (const tabEl of tabEls) {
const id = tabEl.getAttribute("data-bs-target");
if (id) {
const columnEl = document.querySelector(
`${id} .column-margin, .tabset-margin-content`
);
if (columnEl)
tabEl.addEventListener("shown.bs.tab", function (event) {
const el = event.srcElement;
if (el) {
const visibleCls = `${el.id}-margin-content`;
// walk up until we find a parent tabset
let panelTabsetEl = el.parentElement;
while (panelTabsetEl) {
if (panelTabsetEl.classList.contains("panel-tabset")) {
break;
}
panelTabsetEl = panelTabsetEl.parentElement;
}
if (panelTabsetEl) {
const prevSib = panelTabsetEl.previousElementSibling;
if (
prevSib &&
prevSib.classList.contains("tabset-margin-container")
) {
const childNodes = prevSib.querySelectorAll(
".tabset-margin-content"
);
for (const childEl of childNodes) {
if (childEl.classList.contains(visibleCls)) {
childEl.classList.remove("collapse");
} else {
childEl.classList.add("collapse");
}
}
}
}
}
layoutMarginEls();
});
}
}
// Manage the visibility of the toc and the sidebar
const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, {
id: "quarto-toc-toggle",
titleSelector: "#toc-title",
dismissOnClick: true,
});
const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, {
id: "quarto-sidebarnav-toggle",
titleSelector: ".title",
dismissOnClick: false,
});
let tocLeftScrollVisibility;
if (leftTocEl) {
tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, {
id: "quarto-lefttoc-toggle",
titleSelector: "#toc-title",
dismissOnClick: true,
});
}
// Find the first element that uses formatting in special columns
const conflictingEls = window.document.body.querySelectorAll(
'[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]'
);
// Filter all the possibly conflicting elements into ones
// the do conflict on the left or ride side
const arrConflictingEls = Array.from(conflictingEls);
const leftSideConflictEls = arrConflictingEls.filter((el) => {
if (el.tagName === "ASIDE") {
return false;
}
return Array.from(el.classList).find((className) => {
return (
className !== "column-body" &&
className.startsWith("column-") &&
!className.endsWith("right") &&
!className.endsWith("container") &&
className !== "column-margin"
);
});
});
const rightSideConflictEls = arrConflictingEls.filter((el) => {
if (el.tagName === "ASIDE") {
return true;
}
const hasMarginCaption = Array.from(el.classList).find((className) => {
return className == "margin-caption";
});
if (hasMarginCaption) {
return true;
}
return Array.from(el.classList).find((className) => {
return (
className !== "column-body" &&
!className.endsWith("container") &&
className.startsWith("column-") &&
!className.endsWith("left")
);
});
});
const kOverlapPaddingSize = 10;
function toRegions(els) {
return els.map((el) => {
const boundRect = el.getBoundingClientRect();
const top =
boundRect.top +
document.documentElement.scrollTop -
kOverlapPaddingSize;
return {
top,
bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize,
};
});
}
let hasObserved = false;
const visibleItemObserver = (els) => {
let visibleElements = [...els];
const intersectionObserver = new IntersectionObserver(
(entries, _observer) => {
entries.forEach((entry) => {
if (entry.isIntersecting) {
if (visibleElements.indexOf(entry.target) === -1) {
visibleElements.push(entry.target);
}
} else {
visibleElements = visibleElements.filter((visibleEntry) => {
return visibleEntry !== entry;
});
}
});
if (!hasObserved) {
hideOverlappedSidebars();
}
hasObserved = true;
},
{}
);
els.forEach((el) => {
intersectionObserver.observe(el);
});
return {
getVisibleEntries: () => {
return visibleElements;
},
};
};
const rightElementObserver = visibleItemObserver(rightSideConflictEls);
const leftElementObserver = visibleItemObserver(leftSideConflictEls);
const hideOverlappedSidebars = () => {
marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries()));
sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries()));
if (tocLeftScrollVisibility) {
tocLeftScrollVisibility(
toRegions(leftElementObserver.getVisibleEntries())
);
}
};
window.quartoToggleReader = () => {
// Applies a slow class (or removes it)
// to update the transition speed
const slowTransition = (slow) => {
const manageTransition = (id, slow) => {
const el = document.getElementById(id);
if (el) {
if (slow) {
el.classList.add("slow");
} else {
el.classList.remove("slow");
}
}
};
manageTransition("TOC", slow);
manageTransition("quarto-sidebar", slow);
};
const readerMode = !isReaderMode();
setReaderModeValue(readerMode);
// If we're entering reader mode, slow the transition
if (readerMode) {
slowTransition(readerMode);
}
highlightReaderToggle(readerMode);
hideOverlappedSidebars();
// If we're exiting reader mode, restore the non-slow transition
if (!readerMode) {
slowTransition(!readerMode);
}
};
const highlightReaderToggle = (readerMode) => {
const els = document.querySelectorAll(".quarto-reader-toggle");
if (els) {
els.forEach((el) => {
if (readerMode) {
el.classList.add("reader");
} else {
el.classList.remove("reader");
}
});
}
};
const setReaderModeValue = (val) => {
if (window.location.protocol !== "file:") {
window.localStorage.setItem("quarto-reader-mode", val);
} else {
localReaderMode = val;
}
};
const isReaderMode = () => {
if (window.location.protocol !== "file:") {
return window.localStorage.getItem("quarto-reader-mode") === "true";
} else {
return localReaderMode;
}
};
let localReaderMode = null;
const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded");
const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1;
// Walk the TOC and collapse/expand nodes
// Nodes are expanded if:
// - they are top level
// - they have children that are 'active' links
// - they are directly below an link that is 'active'
const walk = (el, depth) => {
// Tick depth when we enter a UL
if (el.tagName === "UL") {
depth = depth + 1;
}
// It this is active link
let isActiveNode = false;
if (el.tagName === "A" && el.classList.contains("active")) {
isActiveNode = true;
}
// See if there is an active child to this element
let hasActiveChild = false;
for (const child of el.children) {
hasActiveChild = walk(child, depth) || hasActiveChild;
}
// Process the collapse state if this is an UL
if (el.tagName === "UL") {
if (tocOpenDepth === -1 && depth > 1) {
// toc-expand: false
el.classList.add("collapse");
} else if (
depth <= tocOpenDepth ||
hasActiveChild ||
prevSiblingIsActiveLink(el)
) {
el.classList.remove("collapse");
} else {
el.classList.add("collapse");
}
// untick depth when we leave a UL
depth = depth - 1;
}
return hasActiveChild || isActiveNode;
};
// walk the TOC and expand / collapse any items that should be shown
if (tocEl) {
updateActiveLink();
walk(tocEl, 0);
}
// Throttle the scroll event and walk peridiocally
window.document.addEventListener(
"scroll",
throttle(() => {
if (tocEl) {
updateActiveLink();
walk(tocEl, 0);
}
if (!isReaderMode()) {
hideOverlappedSidebars();
}
}, 5)
);
window.addEventListener(
"resize",
throttle(() => {
if (tocEl) {
updateActiveLink();
walk(tocEl, 0);
}
if (!isReaderMode()) {
hideOverlappedSidebars();
}
}, 10)
);
hideOverlappedSidebars();
highlightReaderToggle(isReaderMode());
});
tabsets.init();
axe.init();
function throttle(func, wait) {
let waiting = false;
return function () {
if (!waiting) {
func.apply(this, arguments);
waiting = true;
setTimeout(function () {
waiting = false;
}, wait);
}
};
}
function nexttick(func) {
return setTimeout(func, 0);
}
Readme_files/libs/quarto-html/tabsets/tabsets.js
-95
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@@ -1,95 +0,0 @@
// grouped tabsets
export function init() {
window.addEventListener("pageshow", (_event) => {
function getTabSettings() {
const data = localStorage.getItem("quarto-persistent-tabsets-data");
if (!data) {
localStorage.setItem("quarto-persistent-tabsets-data", "{}");
return {};
}
if (data) {
return JSON.parse(data);
}
}
function setTabSettings(data) {
localStorage.setItem(
"quarto-persistent-tabsets-data",
JSON.stringify(data)
);
}
function setTabState(groupName, groupValue) {
const data = getTabSettings();
data[groupName] = groupValue;
setTabSettings(data);
}
function toggleTab(tab, active) {
const tabPanelId = tab.getAttribute("aria-controls");
const tabPanel = document.getElementById(tabPanelId);
if (active) {
tab.classList.add("active");
tabPanel.classList.add("active");
} else {
tab.classList.remove("active");
tabPanel.classList.remove("active");
}
}
function toggleAll(selectedGroup, selectorsToSync) {
for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) {
const active = selectedGroup === thisGroup;
for (const tab of tabs) {
toggleTab(tab, active);
}
}
}
function findSelectorsToSyncByLanguage() {
const result = {};
const tabs = Array.from(
document.querySelectorAll(`div[data-group] a[id^='tabset-']`)
);
for (const item of tabs) {
const div = item.parentElement.parentElement.parentElement;
const group = div.getAttribute("data-group");
if (!result[group]) {
result[group] = {};
}
const selectorsToSync = result[group];
const value = item.innerHTML;
if (!selectorsToSync[value]) {
selectorsToSync[value] = [];
}
selectorsToSync[value].push(item);
}
return result;
}
function setupSelectorSync() {
const selectorsToSync = findSelectorsToSyncByLanguage();
Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => {
Object.entries(tabSetsByValue).forEach(([value, items]) => {
items.forEach((item) => {
item.addEventListener("click", (_event) => {
setTabState(group, value);
toggleAll(value, selectorsToSync[group]);
});
});
});
});
return selectorsToSync;
}
const selectorsToSync = setupSelectorSync();
for (const [group, selectedName] of Object.entries(getTabSettings())) {
const selectors = selectorsToSync[group];
// it's possible that stale state gives us empty selections, so we explicitly check here.
if (selectors) {
toggleAll(selectedName, selectors);
}
}
});
}
Readme_files/libs/quarto-html/tippy.css
-1
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@@ -1 +0,0 @@
.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 10px)}.tippy-box{position:relative;background-color:#333;color:#fff;border-radius:4px;font-size:14px;line-height:1.4;white-space:normal;outline:0;transition-property:transform,visibility,opacity}.tippy-box[data-placement^=top]>.tippy-arrow{bottom:0}.tippy-box[data-placement^=top]>.tippy-arrow:before{bottom:-7px;left:0;border-width:8px 8px 0;border-top-color:initial;transform-origin:center top}.tippy-box[data-placement^=bottom]>.tippy-arrow{top:0}.tippy-box[data-placement^=bottom]>.tippy-arrow:before{top:-7px;left:0;border-width:0 8px 8px;border-bottom-color:initial;transform-origin:center bottom}.tippy-box[data-placement^=left]>.tippy-arrow{right:0}.tippy-box[data-placement^=left]>.tippy-arrow:before{border-width:8px 0 8px 8px;border-left-color:initial;right:-7px;transform-origin:center left}.tippy-box[data-placement^=right]>.tippy-arrow{left:0}.tippy-box[data-placement^=right]>.tippy-arrow:before{left:-7px;border-width:8px 8px 8px 0;border-right-color:initial;transform-origin:center right}.tippy-box[data-inertia][data-state=visible]{transition-timing-function:cubic-bezier(.54,1.5,.38,1.11)}.tippy-arrow{width:16px;height:16px;color:#333}.tippy-arrow:before{content:"";position:absolute;border-color:transparent;border-style:solid}.tippy-content{position:relative;padding:5px 9px;z-index:1}
Readme_files/libs/quarto-html/tippy.umd.min.js
Vendored
-2
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@@ -1,2 +0,0 @@
!function(e,t){"object"==typeof exports&&"undefined"!=typeof module?module.exports=t(require("@popperjs/core")):"function"==typeof define&&define.amd?define(["@popperjs/core"],t):(e=e||self).tippy=t(e.Popper)}(this,(function(e){"use strict";var t={passive:!0,capture:!0},n=function(){return document.body};function r(e,t,n){if(Array.isArray(e)){var r=e[t];return null==r?Array.isArray(n)?n[t]:n:r}return e}function o(e,t){var n={}.toString.call(e);return 0===n.indexOf("[object")&&n.indexOf(t+"]")>-1}function i(e,t){return"function"==typeof e?e.apply(void 0,t):e}function a(e,t){return 0===t?e:function(r){clearTimeout(n),n=setTimeout((function(){e(r)}),t)};var n}function s(e,t){var n=Object.assign({},e);return t.forEach((function(e){delete n[e]})),n}function u(e){return[].concat(e)}function c(e,t){-1===e.indexOf(t)&&e.push(t)}function p(e){return e.split("-")[0]}function f(e){return[].slice.call(e)}function l(e){return Object.keys(e).reduce((function(t,n){return void 0!==e[n]&&(t[n]=e[n]),t}),{})}function d(){return document.createElement("div")}function v(e){return["Element","Fragment"].some((function(t){return o(e,t)}))}function m(e){return o(e,"MouseEvent")}function g(e){return!(!e||!e._tippy||e._tippy.reference!==e)}function h(e){return v(e)?[e]:function(e){return o(e,"NodeList")}(e)?f(e):Array.isArray(e)?e:f(document.querySelectorAll(e))}function b(e,t){e.forEach((function(e){e&&(e.style.transitionDuration=t+"ms")}))}function y(e,t){e.forEach((function(e){e&&e.setAttribute("data-state",t)}))}function w(e){var t,n=u(e)[0];return null!=n&&null!=(t=n.ownerDocument)&&t.body?n.ownerDocument:document}function E(e,t,n){var r=t+"EventListener";["transitionend","webkitTransitionEnd"].forEach((function(t){e[r](t,n)}))}function O(e,t){for(var n=t;n;){var r;if(e.contains(n))return!0;n=null==n.getRootNode||null==(r=n.getRootNode())?void 0:r.host}return!1}var x={isTouch:!1},C=0;function T(){x.isTouch||(x.isTouch=!0,window.performance&&document.addEventListener("mousemove",A))}function A(){var e=performance.now();e-C<20&&(x.isTouch=!1,document.removeEventListener("mousemove",A)),C=e}function L(){var e=document.activeElement;if(g(e)){var t=e._tippy;e.blur&&!t.state.isVisible&&e.blur()}}var D=!!("undefined"!=typeof window&&"undefined"!=typeof document)&&!!window.msCrypto,R=Object.assign({appendTo:n,aria:{content:"auto",expanded:"auto"},delay:0,duration:[300,250],getReferenceClientRect:null,hideOnClick:!0,ignoreAttributes:!1,interactive:!1,interactiveBorder:2,interactiveDebounce:0,moveTransition:"",offset:[0,10],onAfterUpdate:function(){},onBeforeUpdate:function(){},onCreate:function(){},onDestroy:function(){},onHidden:function(){},onHide:function(){},onMount:function(){},onShow:function(){},onShown:function(){},onTrigger:function(){},onUntrigger:function(){},onClickOutside:function(){},placement:"top",plugins:[],popperOptions:{},render:null,showOnCreate:!1,touch:!0,trigger:"mouseenter focus",triggerTarget:null},{animateFill:!1,followCursor:!1,inlinePositioning:!1,sticky:!1},{allowHTML:!1,animation:"fade",arrow:!0,content:"",inertia:!1,maxWidth:350,role:"tooltip",theme:"",zIndex:9999}),k=Object.keys(R);function P(e){var t=(e.plugins||[]).reduce((function(t,n){var r,o=n.name,i=n.defaultValue;o&&(t[o]=void 0!==e[o]?e[o]:null!=(r=R[o])?r:i);return t}),{});return Object.assign({},e,t)}function j(e,t){var n=Object.assign({},t,{content:i(t.content,[e])},t.ignoreAttributes?{}:function(e,t){return(t?Object.keys(P(Object.assign({},R,{plugins:t}))):k).reduce((function(t,n){var r=(e.getAttribute("data-tippy-"+n)||"").trim();if(!r)return t;if("content"===n)t[n]=r;else try{t[n]=JSON.parse(r)}catch(e){t[n]=r}return t}),{})}(e,t.plugins));return n.aria=Object.assign({},R.aria,n.aria),n.aria={expanded:"auto"===n.aria.expanded?t.interactive:n.aria.expanded,content:"auto"===n.aria.content?t.interactive?null:"describedby":n.aria.content},n}function M(e,t){e.innerHTML=t}function V(e){var t=d();return!0===e?t.className="tippy-arrow":(t.className="tippy-svg-arrow",v(e)?t.appendChild(e):M(t,e)),t}function I(e,t){v(t.content)?(M(e,""),e.appendChild(t.content)):"function"!=typeof t.content&&(t.allowHTML?M(e,t.content):e.textContent=t.content)}function S(e){var t=e.firstElementChild,n=f(t.children);return{box:t,content:n.find((function(e){return e.classList.contains("tippy-content")})),arrow:n.find((function(e){return e.classList.contains("tippy-arrow")||e.classList.contains("tippy-svg-arrow")})),backdrop:n.find((function(e){return e.classList.contains("tippy-backdrop")}))}}function N(e){var t=d(),n=d();n.className="tippy-box",n.setAttribute("data-state","hidden"),n.setAttribute("tabindex","-1");var r=d();function o(n,r){var o=S(t),i=o.box,a=o.content,s=o.arrow;r.theme?i.setAttribute("data-theme",r.theme):i.removeAttribute("data-theme"),"string"==typeof r.animation?i.setAttribute("data-animation",r.animation):i.removeAttribute("data-animation"),r.inertia?i.setAttribute("data-inertia",""):i.removeAttribute("data-inertia"),i.style.maxWidth="number"==tyLine truncated
jupyterhub_volumes/course/data/Wolf_diet/wolf_F.fastq
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jupyterhub_volumes/web/.gitignore
+1 -2
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@@ -1,4 +1,3 @@
/.quarto/
**/*.quarto_ipynb
/pages/
/obidoc/
/pages/
jupyterhub_volumes/web/obidoc/404.html
+56
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@@ -0,0 +1,56 @@
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="">
<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/404.html">
<meta property="og:site_name" content="OBITools4 documentation">
<meta property="og:title" content="404 Page not found">
<meta property="og:locale" content="en_us">
<meta property="og:type" content="website">
<title>404 Page not found | OBITools4 documentation</title>
<link rel="icon" href="/obidoc/favicon.png" >
<link rel="manifest" href="/obidoc/manifest.json">
<link rel="canonical" href="http://metabar:8888/obidoc/404.html">
<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb&#43;a3g=" crossorigin="anonymous">
<script defer src="/obidoc/fuse.min.js"></script>
<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq&#43;Or85BgKocXepm2Z&#43;ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
<!--
Made with Book Theme
https://github.com/alex-shpak/hugo-book
-->
<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
<style>
.not-found {
text-align: center;
}
.not-found h1 {
margin: .25em 0 0 0;
opacity: .25;
font-size: 40vmin;
}
</style>
</head>
<body>
<main class="flex justify-center not-found">
<div>
<h1>404</h1>
<h2>Page Not Found</h2>
<h3>
<a href="/obidoc/">OBITools4 documentation</a>
</h3>
</div>
</main>
</body>
</html>
jupyterhub_volumes/web/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css
+1
View File
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jupyterhub_volumes/web/obidoc/docs/commands/alignments/obipairing/exact-alignment/pairing_score.qmd
+149
View File
@@ -0,0 +1,149 @@
---
title: "Untitled"
format: html
editor: visual
---
```{r}
library(tidyverse)
library(plotly)
library(matrixStats)
```
```{r}
log_sum_exp <- function(a,b) {
m <- map2_dbl(a,b,max)
m + log(exp(a-m)+exp(b-m))
}
```
$$
\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
$$
```{r}
log1m_exp <- function(b) {
if (any(b >= 0)) {
stop(glue::glue("b must be negative (b={b})"))
}
return(log(-expm1(b))) # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
}
```
$$
\log(e^a - e^b) = a + \log(1 - e^{b-a})
$$
```{r}
log_diff_exp <- function(a, b) {
# Vérifier si a > b pour éviter des résultats indéfinis
if (any(a < b)) {
stop(glue::glue("Erreur : a ({a}) doit etre strictement sup�rieur � b ({b}) pour que e^a - e^b soit positif."))
}
# Calculer log(e^a - e^b) de manière stable
ifelse(a == b, -Inf,a + log1m_exp(b-a))
}
```
$$
P_{error} = 10^{-\frac{Q}{10}}
$$
$$
\begin{aligned}
q_F &= -\frac{Q_F}{10} \cdot \log(10) \\
q_R &= -\frac{Q_R}{10} \cdot \log(10) \\
P(macth | Obs(match)) &= (1-e^{q_F}) (1-e^{q_R}) + (1-e^{q_F})\frac{e^{q_R}}{4}+ (1-e^{q_R})\frac{e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
&=1 - e^{q_R} - e^{q_F} + e^{q_F+q_R} + \frac{e^{q_R}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F}}{4} - \frac{e^{q_F+q_R}}{4} + \frac{e^{q_F+q_R}}{4} \\
&= \frac{4 - 4e^{q_F} - 4e^{q_R} + 4e^{q_F+q_R} + e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4} \\
&= \frac{4 - 3e^{q_F}- 3e^{q_R} + 3e^{q_F+q_R}}{4}\\
&= \frac{4 - 3(e^{q_F}+e^{q_R}-e^{q_F+q_R})}{4} \\
&= 1 - \frac{3}{4}\left(e^{q_F}+e^{q_R}-e^{q_F+q_R}\right)
\end{aligned}
$$
```{r}
Pm_match_observed <- function(Q_F, Q_R) {
l10 <- log(10)
l3 <- log(3)
l4 <- log(4)
q_F <- -Q_F/10*l10
q_R <- -Q_R/10*l10
term1 <- log_sum_exp(q_F,q_R)
term2 <- log_diff_exp(term1,q_F+q_R) + l3 - l4
log1m_exp(term2)
}
```
$$
\begin{aligned}
P(macth | Obs(mismatch)) &= \frac{(1-e^{q_F})e^{q_R}}{4} + \frac{(1-e^{q_R})e^{q_F}}{4} + \frac{e^{q_F+q_R}}{4} \\
&= \frac{(1-e^{q_F})e^{q_R} + (1-e^{q_R})e^{q_F} + e^{q_F+q_R}}{4} \\
&= \frac{e^{q_R} - e^{q_F+q_R} + e^{q_F} - e^{q_F+q_R} + e^{q_F+q_R}}{4} \\
&= \frac{e^{q_F} + e^{q_R} - e^{q_F+q_R}}{4}
\end{aligned}
$$
```{r}
Pm_mismatch_observed <- function(Q_F, Q_R) {
l10 <- log(10)
l3 <- log(3)
l4 <- log(4)
q_F <- -Q_F/10*l10
q_R <- -Q_R/10*l10
term1 <- log_sum_exp(q_F,q_R)
log_diff_exp(term1,q_F+q_R) - l4
}
```
```{r}
score_match_observed <- function(Q_F, Q_R) {
Pm_match_observed(Q_F,Q_R) - log1m_exp(Pm_match_observed(Q_F,Q_R))
}
score_mismatch_observed <- function(Q_F, Q_R) {
Pm_mismatch_observed(Q_F,Q_R) - log1m_exp(Pm_mismatch_observed(Q_F,Q_R))
}
```
```{r}
scores <- expand_grid(QF=0:40,QR=0:40) %>%
mutate(score_match_observed = round(score_match_observed(QF,QR),2),
score_mismatch_observed = round(score_mismatch_observed(QF,QR),2))
```
```{r}
plot_match <- plot_ly(scores,
x=~QF, y=~QR, z=~score_match_observed,
type="mesh3d") %>%
layout(
plot_bgcolor = "#bababa",
scene = list(
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
yaxis = list(title = "Q reverse read"),
zaxis = list(title = "Score match")))
```
```{r}
plot_mismatch <- plot_ly(scores,
x=~QF, y=~QR, z=~score_mismatch_observed,
type="mesh3d") %>%
layout(
plot_bgcolor = "#bababa",
scene = list(
xaxis = list(title = "Q forward read"), # Change x/y/z axis title
yaxis = list(title = "Q reverse read"),
zaxis = list(title = "Score mismatch")))
```
```{r}
write(plotly_json(plot_match,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/match.json")
write(plotly_json(plot_mismatch,FALSE),"content/docs/commands/alignments/obipairing/exact-alignment/mismatch.json")
```
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#!/usr/bin/env python3
import re
import gzip
import struct
import sys
import time
import getopt
from functools import cmp_to_key
_dbenable=False
#####
#
#
# Generic file function
#
#
#####
def universalOpen(file):
if isinstance(file,str):
if file[-3:] == '.gz':
rep = gzip.open(file)
else:
rep = open(file)
else:
rep = file
return rep
def universalTell(file):
if isinstance(file, gzip.GzipFile):
file=file.myfileobj
return file.tell()
def fileSize(file):
if isinstance(file, gzip.GzipFile):
file=file.myfileobj
pos = file.tell()
file.seek(0,2)
length = file.tell()
file.seek(pos,0)
return length
def progressBar(pos,max,reset=False,delta=[]):
if reset:
del delta[:]
if not delta:
delta.append(time.time())
delta.append(time.time())
delta[1]=time.time()
elapsed = delta[1]-delta[0]
percent = float(pos)/max * 100
remain = time.strftime('%H:%M:%S',time.gmtime(elapsed / percent * (100-percent)))
bar = '#' * int(percent/2)
bar+= '|/-\\-'[pos % 5]
bar+= ' ' * (50 - int(percent/2))
sys.stderr.write('\r%5.1f %% |%s] remain : %s' %(percent,bar,remain))
#####
#
#
# NCBI Dump Taxonomy reader
#
#
#####
def endLessIterator(endedlist):
for x in endedlist:
yield x
while(1):
yield endedlist[-1]
class ColumnFile(object):
def __init__(self,stream,sep=None,strip=True,types=None):
if isinstance(stream,str):
self._stream = open(stream)
else:
try:
iter(stream)
self._stream = stream
except TypeError:
raise ValueError('stream must be string or an iterator')
self._delimiter=sep
self._strip=strip
if types:
self._types=[x for x in types]
for i in range(len(self._types)):
if self._types[i] is bool:
self._types[i]=ColumnFile.str2bool
else:
self._types=None
def str2bool(x):
return bool(eval(x.strip()[0].upper(),{'T':True,'V':True,'F':False}))
str2bool = staticmethod(str2bool)
def __iter__(self):
return self
def __next__(self):
ligne = next(self._stream)
data = ligne.split(self._delimiter)
if self._strip or self._types:
data = [x.strip() for x in data]
if self._types:
it = endLessIterator(self._types)
data = [x[1](x[0]) for x in ((y,next(it)) for y in data)]
return data
def taxonCmp(t1,t2):
if t1[0] < t2[0]:
return -1
elif t1[0] > t2[0]:
return +1
return 0
def bsearchTaxon(taxonomy,taxid):
taxCount = len(taxonomy)
begin = 0
end = taxCount
oldcheck=taxCount
check = int(begin + end / 2)
while check != oldcheck and taxonomy[check][0]!=taxid :
if taxonomy[check][0] < taxid:
begin=check
else:
end=check
oldcheck=check
check = int((begin + end) / 2)
if taxonomy[check][0]==taxid:
return check
else:
return None
def readNodeTable(file):
file = universalOpen(file)
nodes = ColumnFile(file,
sep='|',
types=(int,int,str,
str,str,bool,
int,bool,int,
bool,bool,bool,str))
print("Reading taxonomy dump file...", file=sys.stderr)
taxonomy=[[n[0],n[2],n[1]] for n in nodes]
print("List all taxonomy rank...", file=sys.stderr)
ranks =list(set(x[1] for x in taxonomy))
ranks.sort()
ranks = {rank: index for index, rank in enumerate(ranks)}
print("Sorting taxons...", file=sys.stderr)
taxonomy.sort(key=lambda x: x[0])
print("Indexing taxonomy...", file=sys.stderr)
index = {}
for t in taxonomy:
index[t[0]]=bsearchTaxon(taxonomy, t[0])
print("Indexing parent and rank...", file=sys.stderr)
for t in taxonomy:
t[1]=ranks[t[1]]
t[2]=index[t[2]]
return taxonomy,ranks,index
def nameIterator(file):
file = universalOpen(file)
names = ColumnFile(file,
sep='|',
types=(int,str,
str,str))
for taxid,name,unique,classname,white in names:
yield taxid,name,classname
def mergedNodeIterator(file):
file = universalOpen(file)
merged = ColumnFile(file,
sep='|',
types=(int,int,str))
for taxid,current,white in merged:
yield taxid,current
def deletedNodeIterator(file):
file = universalOpen(file)
deleted = ColumnFile(file,
sep='|',
types=(int,str))
for taxid,white in deleted:
yield taxid
def readTaxonomyDump(taxdir):
taxonomy,ranks,index = readNodeTable('%s/nodes.dmp' % taxdir)
print("Adding scientific name...", file=sys.stderr)
alternativeName=[]
for taxid,name,classname in nameIterator('%s/names.dmp' % taxdir):
alternativeName.append((name,classname,index[taxid]))
if classname == 'scientific name':
taxonomy[index[taxid]].append(name)
print("Adding taxid alias...", file=sys.stderr)
for taxid,current in mergedNodeIterator('%s/merged.dmp' % taxdir):
index[taxid]=index[current]
print("Adding deleted taxid...", file=sys.stderr)
for taxid in deletedNodeIterator('%s/delnodes.dmp' % taxdir):
index[taxid]=None
return taxonomy,ranks,alternativeName,index
#####
#
#
# Genbank/EMBL sequence reader
#
#
#####
def entryIterator(file):
file = universalOpen(file)
rep =[]
ligne = file.readline()
while ligne:
rep.append(ligne)
if ligne == '//\n':
rep = ''.join(rep)
yield rep
rep = []
ligne = file.readline()
def fastaEntryIterator(file):
file = universalOpen(file)
rep =[]
ligne = file.readline()
while ligne:
if ligne[0] == '>' and rep:
rep = ''.join(rep)
yield rep
rep = []
rep.append(ligne)
ligne = file.readline()
if rep:
rep = ''.join(rep)
yield rep
_cleanSeq = re.compile('[ \n0-9]+')
def cleanSeq(seq):
return _cleanSeq.sub('',seq)
_gbParseID = re.compile('(?<=^LOCUS {7})[^ ]+(?= )',re.MULTILINE)
_gbParseDE = re.compile('(?<=^DEFINITION {2}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
_gbParseSQ = re.compile('(?<=^ORIGIN).+?(?=^//$)',re.MULTILINE+re.DOTALL)
_gbParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
def genbankEntryParser(entry):
Id = _gbParseID.findall(entry)[0]
De = ' '.join(_gbParseDE.findall(entry)[0].split())
Sq = cleanSeq(_gbParseSQ.findall(entry)[0].upper())
try:
Tx = int(_gbParseTX.findall(entry)[0])
except IndexError:
Tx = None
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
######################
_cleanDef = re.compile('[\nDE]')
def cleanDef(definition):
return _cleanDef.sub('',definition)
_emblParseID = re.compile('(?<=^ID {3})[^ ]+(?=;)',re.MULTILINE)
_emblParseDE = re.compile('(?<=^DE {3}).+?\\. *$(?=[^ ])',re.MULTILINE+re.DOTALL)
_emblParseSQ = re.compile('(?<=^ ).+?(?=^//$)',re.MULTILINE+re.DOTALL)
_emblParseTX = re.compile('(?<= /db_xref="taxon:)[0-9]+(?=")')
def emblEntryParser(entry):
Id = _emblParseID.findall(entry)[0]
De = ' '.join(cleanDef(_emblParseDE.findall(entry)[0]).split())
Sq = cleanSeq(_emblParseSQ.findall(entry)[0].upper())
try:
Tx = int(_emblParseTX.findall(entry)[0])
except IndexError:
Tx = None
return {'id':Id,'taxid':Tx,'definition':De,'sequence':Sq}
######################
_fastaSplit=re.compile(';\\W*')
def parseFasta(seq):
seq=seq.split('\n')
title = seq[0].strip()[1:].split(None,1)
id=title[0]
if len(title) == 2:
field = _fastaSplit.split(title[1])
else:
field=[]
info = dict(x.split('=',1) for x in field if '=' in x)
definition = ' '.join([x for x in field if '=' not in x])
seq=(''.join([x.strip() for x in seq[1:]])).upper()
return id,seq,definition,info
def fastaEntryParser(entry):
id,seq,definition,info = parseFasta(entry)
Tx = info.get('taxid',None)
if Tx is not None:
match = re.search(r'taxon:(\d+)', Tx)
if match:
Tx = match.group(1)
Tx=int(Tx)
return {'id':id,'taxid':Tx,'definition':definition,'sequence':seq}
def sequenceIteratorFactory(entryParser,entryIterator):
def sequenceIterator(file):
for entry in entryIterator(file):
yield entryParser(entry)
return sequenceIterator
def taxonomyInfo(entry,connection):
taxid = entry['taxid']
curseur = connection.cursor()
curseur.execute("""
select taxid,species,genus,family,
taxonomy.scientificName(taxid) as sn,
taxonomy.scientificName(species) as species_sn,
taxonomy.scientificName(genus) as genus_sn,
taxonomy.scientificName(family) as family_sn
from
(
select alias as taxid,
taxonomy.getSpecies(alias) as species,
taxonomy.getGenus(alias) as genus,
taxonomy.getFamily(alias) as family
from taxonomy.aliases
where id=%d ) as tax
""" % taxid)
rep = curseur.fetchone()
entry['current_taxid']=rep[0]
entry['species']=rep[1]
entry['genus']=rep[2]
entry['family']=rep[3]
entry['scientific_name']=rep[4]
entry['species_sn']=rep[5]
entry['genus_sn']=rep[6]
entry['family_sn']=rep[7]
return entry
#####
#
#
# Binary writer
#
#
#####
def ecoSeqPacker(sq):
compactseq = gzip.zlib.compress(bytes(sq['sequence'],"ascii"),9)
cptseqlength = len(compactseq)
delength = len(sq['definition'])
totalSize = 4 + 20 + 4 + 4 + 4 + cptseqlength + delength
packed = struct.pack('> I I 20s I I I %ds %ds' % (delength,cptseqlength),
totalSize,
sq['taxid'],
bytes(sq['id'],"ascii"),
delength,
len(sq['sequence']),
cptseqlength,
bytes(sq['definition'],"ascii"),
compactseq)
assert len(packed) == totalSize+4, "error in sequence packing"
return packed
def ecoTaxPacker(tx):
namelength = len(tx[3])
totalSize = 4 + 4 + 4 + 4 + namelength
packed = struct.pack('> I I I I I %ds' % namelength,
totalSize,
tx[0],
tx[1],
tx[2],
namelength,
bytes(tx[3],"ascii"))
return packed
def ecoRankPacker(rank):
namelength = len(rank)
packed = struct.pack('> I %ds' % namelength,
namelength,
bytes(rank, 'ascii'))
return packed
def ecoNamePacker(name):
namelength = len(name[0])
classlength= len(name[1])
totalSize = namelength + classlength + 4 + 4 + 4 + 4
packed = struct.pack('> I I I I I %ds %ds' % (namelength,classlength),
totalSize,
int(name[1]=='scientific name'),
namelength,
classlength,
name[2],
bytes(name[0], 'ascii'),
bytes(name[1], 'ascii'))
return packed
def ecoSeqWriter(file,input,taxindex,parser):
output = open(file,'wb')
input = universalOpen(input)
inputsize = fileSize(input)
entries = parser(input)
seqcount=0
skipped = []
output.write(struct.pack('> I',seqcount))
progressBar(1, inputsize,reset=True)
for entry in entries:
if entry['taxid'] is not None:
try:
entry['taxid']=taxindex[entry['taxid']]
except KeyError:
entry['taxid']=None
if entry['taxid'] is not None:
seqcount+=1
output.write(ecoSeqPacker(entry))
else:
skipped.append(entry['id'])
where = universalTell(input)
progressBar(where, inputsize)
print(" Readed sequences : %d " % seqcount, end=' ', file=sys.stderr)
else:
skipped.append(entry['id'])
print(file=sys.stderr)
output.seek(0,0)
output.write(struct.pack('> I',seqcount))
output.close()
return skipped
def ecoTaxWriter(file,taxonomy):
output = open(file,'wb')
output.write(struct.pack('> I',len(taxonomy)))
for tx in taxonomy:
output.write(ecoTaxPacker(tx))
output.close()
def ecoRankWriter(file,ranks):
output = open(file,'wb')
output.write(struct.pack('> I',len(ranks)))
rankNames = list(ranks.keys())
rankNames.sort()
for rank in rankNames:
output.write(ecoRankPacker(rank))
output.close()
def nameCmp(n1,n2):
name1=n1[0].upper()
name2=n2[0].upper()
if name1 < name2:
return -1
elif name1 > name2:
return 1
return 0
def ecoNameWriter(file,names):
output = open(file,'wb')
output.write(struct.pack('> I',len(names)))
names.sort(key=lambda x:x[0].upper())
for name in names:
output.write(ecoNamePacker(name))
output.close()
def ecoDBWriter(prefix,taxonomy,seqFileNames,parser):
ecoRankWriter('%s.rdx' % prefix, taxonomy[1])
ecoTaxWriter('%s.tdx' % prefix, taxonomy[0])
ecoNameWriter('%s.ndx' % prefix, taxonomy[2])
filecount = 0
for filename in seqFileNames:
filecount+=1
sk=ecoSeqWriter('%s_%03d.sdx' % (prefix,filecount),
filename,
taxonomy[3],
parser)
if sk:
print("Skipped entry :", file=sys.stderr)
print(sk, file=sys.stderr)
def ecoParseOptions(arguments):
opt = {
'prefix' : 'ecodb',
'taxdir' : 'taxdump',
'parser' : sequenceIteratorFactory(genbankEntryParser,
entryIterator)
}
o,filenames = getopt.getopt(arguments,
'ht:T:n:gfe',
['help',
'taxonomy=',
'taxonomy_db=',
'name=',
'genbank',
'fasta',
'embl'])
for name,value in o:
if name in ('-h','--help'):
printHelp()
exit()
elif name in ('-t','--taxonomy'):
opt['taxmod']='dump'
opt['taxdir']=value
elif name in ('-T','--taxonomy_db'):
opt['taxmod']='db'
opt['taxdb']=value
elif name in ('-n','--name'):
opt['prefix']=value
elif name in ('-g','--genbank'):
opt['parser']=sequenceIteratorFactory(genbankEntryParser,
entryIterator)
elif name in ('-f','--fasta'):
opt['parser']=sequenceIteratorFactory(fastaEntryParser,
fastaEntryIterator)
elif name in ('-e','--embl'):
opt['parser']=sequenceIteratorFactory(emblEntryParser,
entryIterator)
else:
raise ValueError('Unknown option %s' % name)
return opt,filenames
def printHelp():
print("-----------------------------------")
print(" ecoPCRFormat.py")
print("-----------------------------------")
print("ecoPCRFormat.py [option] <argument>")
print("-----------------------------------")
print("-e --embl :[E]mbl format")
print("-f --fasta :[F]asta format")
print("-g --genbank :[G]enbank format")
print("-h --help :[H]elp - print this help")
print("-n --name :[N]ame of the new database created")
print("-t --taxonomy :[T]axonomy - path to the taxonomy database")
print(" :bcp-like dump from GenBank taxonomy database.")
print("-----------------------------------")
if __name__ == '__main__':
opt,filenames = ecoParseOptions(sys.argv[1:])
taxonomy = readTaxonomyDump(opt['taxdir'])
ecoDBWriter(opt['prefix'], taxonomy, filenames, opt['parser'])
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<title>Designing new barcodes on OBITools4 documentation</title>
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SHELL := /bin/bash
FTPNCBI=ftp.ncbi.nlm.nih.gov
GBURL=https://$(FTPNCBI)/genbank
GBRELEASE_URL=$(GBURL)/GB_Release_Number
TAXOURL=https://$(FTPNCBI)/pub/taxonomy/taxdump.tar.gz
GBRELEASE:=$(shell curl $(GBRELEASE_URL))
GBDIV_ALL:=$(shell curl -L ${GBURL} \
| grep -E 'gb.+\.seq\.gz' \
| sed -E 's@^.*<a href="gb([^0-9]+)[0-9]+\.seq.gz.*$$@\1@' \
| sort \
| uniq)
GBDIV=bct inv mam phg pln pri rod vrl vrt
DIRECTORIES=fasta fasta_fgs
GBFILE_ALL:=$(shell curl -L ${GBURL} \
| grep -E "gb($$(tr ' ' '|' <<< "${GBDIV}"))[0-9]+" \
| sed -E 's@^<a href="(gb.+.seq.gz)">.*$$@\1@')
SUFFIXES += .d
NODEPS:=clean taxonomy
DEPFILES:=$(wildcard Release_$(GBRELEASE)/depends/*.d)
ifeq (0, $(words $(findstring $(MAKECMDGOALS), $(NODEPS))))
#Chances are, these files don't exist. GMake will create them and
#clean up automatically afterwards
-include $(DEPFILES)
endif
all: depends directories FORCE
@make downloads
downloads: taxonomy fasta_files
@echo Genbank Release number $(GBRELEASE)
@echo all divisions : $(GBDIV_ALL)
FORCE:
@sleep 1
.PHONY: all directories depends taxonomy fasta_files FORCE
depends: directories Release_$(GBRELEASE)/depends/gbfiles.d Makefile
division: $(GBDIV)
taxonomy: directories Release_$(GBRELEASE)/taxonomy
directories: Release_$(GBRELEASE)/fasta Release_$(GBRELEASE)/stamp Release_$(GBRELEASE)/tmp
Release_$(GBRELEASE):
@mkdir -p $@
@echo Create $@ directory
Release_$(GBRELEASE)/fasta: Release_$(GBRELEASE)
@mkdir -p $@
@echo Create $@ directory
Release_$(GBRELEASE)/stamp: Release_$(GBRELEASE)
@mkdir -p $@
@echo Create $@ directory
Release_$(GBRELEASE)/tmp: Release_$(GBRELEASE)
@mkdir -p $@
@echo Create $@ directory
Release_$(GBRELEASE)/depends/gbfiles.d: Makefile
@echo Create depends directory
@mkdir -p Release_$(GBRELEASE)/depends
@for f in ${GBFILE_ALL} ; do \
echo -e "Release_$(GBRELEASE)/stamp/$$f.stamp:" ; \
echo -e "\t@echo Downloading file : $$f..." ; \
echo -e "\t@mkdir -p Release_$(GBRELEASE)/tmp" ; \
echo -e "\t@mkdir -p Release_$(GBRELEASE)/stamp" ; \
echo -e "\t@curl -L ${GBURL}/$$f > Release_$(GBRELEASE)/tmp/$$f && touch \$$@" ; \
echo ; \
div=$$(sed -E 's@^gb(...).*$$@\1@' <<< $$f) ; \
fasta="Release_$(GBRELEASE)/fasta/$$div/$${f/.seq.gz/.fasta.gz}" ; \
fasta_fgs="Release_$(GBRELEASE)/fasta_fgs/$$div/$${f/.seq.gz/.fasta.gz}" ; \
fasta_files="$$fasta_files $$fasta" ; \
fasta_fgs_files="$$fasta_fgs_files $$fasta_fgs" ; \
echo -e "$$fasta: Release_$(GBRELEASE)/stamp/$$f.stamp" ; \
echo -e "\t@echo converting file : \$$< in fasta" ; \
echo -e "\t@mkdir -p Release_$(GBRELEASE)/fasta/$$div" ; \
echo -e "\t@obiconvert -Z --fasta-output --skip-empty \\" ; \
echo -e "\t Release_$(GBRELEASE)/tmp/$$f > Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \\" ; \
echo -e "\t && mv Release_$(GBRELEASE)/tmp/$${f/.seq.gz/.fasta.gz} \$$@ \\" ; \
echo -e "\t && rm -f Release_$(GBRELEASE)/tmp/$$f \\" ; \
echo -e "\t || rm -f \$$@" ; \
echo -e "\t@echo conversion of $$@ done." ; \
echo ; \
done > $@ ; \
echo >> $@ ; \
echo "fasta_files: $$fasta_files" >> $@ ;
Release_$(GBRELEASE)/taxonomy:
mkdir -p $@
curl -iL $(TAXOURL) \
| tar -C $@ -zxf -
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
<channel>
<title>Analysing an Illumina data set on OBITools4 documentation</title>
<link>http://metabar:8888/obidoc/docs/cookbook/illumina/</link>
<description>Recent content in Analysing an Illumina data set on OBITools4 documentation</description>
<generator>Hugo</generator>
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>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:98:16207:5869#0/1_sub[78..81] {"count":2007,"merged_sample":{"29a_F260619":2007},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":2021}}
tttt
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
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>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337}}
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039}}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105}}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789}}
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
gcctaaaactcaaaggacttggtggtgctttacatccct
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ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
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ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
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ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
gcttaaaactcaaaggacttggcggtgccttacgtccct
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ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
gcttaaaactcaaaggacgtggcggtgctttatatccct
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgcttcacaccctt
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ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
gcttaaaactcaaaggacgtggcggtgctttacatccct
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caata
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggtggtgctttctacccct
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcttaaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttacatccct
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
agcccaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaacgcaaaggacttggcggtgctttataccctt
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
agcttaaaactcaaaggacttggcggtgctttatcccctt
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcagtgctttatacccct
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
agcccaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcttaaaactcaaaggacttggcggtgctttatatccct
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ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
gcttaaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcctgaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
gcctaaaactcaaaggacttggtggtgctttacatccct
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ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
gcctaaaactcaaaggacttggcggtgctttacatccct
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ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttatgccctt
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ccgatagg
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ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
gcctaaaactcaaaggacttggcagtgctttacatccct
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
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ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttatatccct
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ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:1:15993:20360#0/1_sub[28..127] {"count":4,"merged_sample":{"13a_F730603":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":4}}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactacctgcaat
agcttaaaactcaaaggacttggcggtgctttatgccctt
>HELIUM_000100422_612GNAAXX:7:103:1205:6990#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":2}}
ttagccctaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:111:2380:10482#0/1_sub[28..126] {"count":2,"merged_sample":{"29a_F260619":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":2}}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaata
gcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:76:10530:11312#0/1_sub[28..126] {"count":43,"merged_sample":{"26a_F040644":43},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":69}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:40:15984:4911#0/1_sub[28..126] {"count":16,"merged_sample":{"26a_F040644":16},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":30}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
gcttaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:109:19171:17424#0/1_sub[28..126] {"count":2,"merged_sample":{"13a_F730603":1,"26a_F040644":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126]":"(a)->(t)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s","26a_F040644":"i"},"obiclean_weight":{"13a_F730603":1,"26a_F040644":1}}
ttagccctaaacatagataattttacaacaaaataattcgccagaggacttctagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:77:17898:19592#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"15a_F730814":"s","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
ttagccctaaacacaagtaattaatataacaaaataattcgccagaggactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:32:4908:16517#0/1_sub[78..81] {"count":7,"merged_sample":{"29a_F260619":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
ccgc
>HELIUM_000100422_612GNAAXX:7:100:8022:19461#0/1_sub[28..127] {"count":5,"merged_sample":{"29a_F260619":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":11}}
ttagccctaaacacaagtaattaatataacaaaataattcgccagagaactactagcaac
agattaaacctcaaaggacttggcagtgctttatacccct
>HELIUM_000100422_612GNAAXX:7:59:2390:15297#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
gcctaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:98:10839:20244#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":2}}
ttagccctaaacataaacattcaataaacaaggatgttcgccagagtactactagcaatg
gcctaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:34:13086:6440#0/1_sub[28..127] {"count":14,"merged_sample":{"13a_F730603":14},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":18}}
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
agcccaaaactcaaaggacttggcggtgcttcacaccctt
>HELIUM_000100422_612GNAAXX:7:73:10944:14101#0/1_sub[28..127] {"count":2,"merged_sample":{"13a_F730603":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":3}}
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:61:17561:21218#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
gcttaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:93:7569:17305#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
ttagccctaaacataaatcagtctataacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:55:11954:15731#0/1_sub[28..126] {"count":6,"merged_sample":{"29a_F260619":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":7}}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376}}
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:54:15067:12524#0/1_sub[28..126] {"count":26,"merged_sample":{"26a_F040644":26},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":49}}
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:6:10451:2548#0/1_sub[28..126] {"count":12,"merged_sample":{"26a_F040644":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":15}}
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaatg
gcctaaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:23:10872:20213#0/1_sub[28..126] {"count":2,"merged_sample":{"26a_F040644":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":3}}
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactagcaaca
gcttaaaactcaaaggacttggcggtgccttacgtccct
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1}}
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:98:6034:5203#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":4}}
ttagccctaaacacaagtaattaatataacaaaattattcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:70:2429:19509#0/1_sub[28..126] {"count":5,"merged_sample":{"26a_F040644":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":5}}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgccttacgtccct
>HELIUM_000100422_612GNAAXX:7:65:1843:2567#0/1_sub[28..126] {"count":7,"merged_sample":{"26a_F040644":7},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":11}}
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:92:1339:19811#0/1_sub[28..127] {"count":3,"merged_sample":{"29a_F260619":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":3}}
ttagccctaaacacaagtaattacacaaacaaaattgttcacaagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:15:13855:1746#0/1_sub[28..127] {"count":3,"merged_sample":{"15a_F730814":2,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:7:14405:19348#0/1_sub[28..127]":"(t)->(g)@51"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":3,"29a_F260619":1}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtgcgaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:7:7092:11003#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":2},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":2}}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacgtccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_assembled_taxo.fasta
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>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_head":true,"obiclean_headcount":2,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":0,"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":4,"obiclean_singletoncount":3,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final.fasta
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>seq0001 {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":1,"taxid":"taxon:9992 [Marmota]@genus"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>seq0002 {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","seq_number":2,"taxid":"taxon:35500 [Pecora]@infraorder"}
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>seq0003 {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":3,"taxid":"taxon:9860 [Cervus elaphus]@species"}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>seq0004 {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","seq_number":4,"taxid":"taxon:337730 [Marmotini]@tribe"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>seq0005 {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","seq_number":5,"taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
>seq0006 {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":6,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>seq0007 {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","seq_number":7,"taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>seq0008 {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","seq_number":8,"taxid":"taxon:9611 [Canis]@genus"}
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_motus.csv
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id,count,obitag_bestid,obitag_bestmatch,obitag_match_count,obitag_rank,obitag_similarity_method,seq_number,taxid,sequence
seq0001,10172,0.9797979797979798,AY227529,1,genus,lcs,1,taxon:9992 [Marmota]@genus,ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
seq0002,260,0.9405940594059405,AF154263,9,infraorder,lcs,2,taxon:35500 [Pecora]@infraorder,ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
seq0003,7146,1,AB245427,1,species,lcs,3,taxon:9860 [Cervus elaphus]@species,ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
seq0004,87,0.9494949494949495,AY227530,2,tribe,lcs,4,taxon:337730 [Marmotini]@tribe,ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
seq0005,95,0.9595959595959596,AC187326,1,subspecies,lcs,5,taxon:9615 [Canis lupus familiaris]@subspecies,ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
seq0006,12004,1,AJ885202,1,species,lcs,6,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
seq0007,319,1,AJ972683,1,species,lcs,7,taxon:9858 [Capreolus capreolus]@species,ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
seq0008,366,1,AB048590,1,genus,lcs,8,taxon:9611 [Canis]@genus,ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
1 id count obitag_bestid obitag_bestmatch obitag_match_count obitag_rank obitag_similarity_method seq_number taxid sequence
2 seq0001 10172 0.9797979797979798 AY227529 1 genus lcs 1 taxon:9992 [Marmota]@genus ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaacagcctgaaactcaaaggacttggcggtgctttacatccct
3 seq0002 260 0.9405940594059405 AF154263 9 infraorder lcs 2 taxon:35500 [Pecora]@infraorder ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaacagcttaaaactcaaaggacttggcggtgctttataccctt
4 seq0003 7146 1 AB245427 1 species lcs 3 taxon:9860 [Cervus elaphus]@species ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
5 seq0004 87 0.9494949494949495 AY227530 2 tribe lcs 4 taxon:337730 [Marmotini]@tribe ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
6 seq0005 95 0.9595959595959596 AC187326 1 subspecies lcs 5 taxon:9615 [Canis lupus familiaris]@subspecies ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaacagattaaacctcaaaggacttggcagtgctttatacccct
7 seq0006 12004 1 AJ885202 1 species lcs 6 taxon:9858 [Capreolus capreolus]@species ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
8 seq0007 319 1 AJ972683 1 species lcs 7 taxon:9858 [Capreolus capreolus]@species ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttataccctt
9 seq0008 366 1 AB048590 1 genus lcs 8 taxon:9611 [Canis]@genus ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaatagcttaaaactcaaaggacttggcggtgctttatatccct
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_final_occurrency.csv
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id,seq0001,seq0002,seq0003,seq0004,seq0005,seq0006,seq0007,seq0008
29a_F260619,0,337,0,0,105,5789,376,1
15a_F730814,0,0,0,0,0,8822,0,5
13a_F730603,0,0,8039,0,0,0,0,17
26a_F040644,12205,0,0,202,12,0,0,468
1 id seq0001 seq0002 seq0003 seq0004 seq0005 seq0006 seq0007 seq0008
2 29a_F260619 0 337 0 0 105 5789 376 1
3 15a_F730814 0 0 0 0 0 8822 0 5
4 13a_F730603 0 0 8039 0 0 0 0 17
5 26a_F040644 12205 0 0 202 12 0 0 468
jupyterhub_volumes/web/obidoc/docs/cookbook/illumina/results/wolf_minimal.fasta
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>HELIUM_000100422_612GNAAXX:7:118:3572:14633#0/1_sub[28..126] {"count":10172,"merged_sample":{"26a_F040644":10172},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":12205},"obitag_bestid":0.9797979797979798,"obitag_bestmatch":"AY227529","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9992 [Marmota]@genus"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
gcctgaaactcaaaggacttggcggtgctttacatccct
>HELIUM_000100422_612GNAAXX:7:99:9351:13090#0/1_sub[28..127] {"count":260,"merged_sample":{"29a_F260619":260},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":337},"obitag_bestid":0.9405940594059405,"obitag_bestmatch":"AF154263","obitag_match_count":9,"obitag_rank":"infraorder","obitag_similarity_method":"lcs","taxid":"taxon:35500 [Pecora]@infraorder"}
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactagcggcaac
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:108:10111:9078#0/1_sub[28..127] {"count":7146,"merged_sample":{"13a_F730603":7146},"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":8039},"obitag_bestid":1,"obitag_bestmatch":"AB245427","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9860 [Cervus elaphus]@species"}
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:38:14204:12725#0/1_sub[28..126] {"count":87,"merged_sample":{"26a_F040644":87},"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":202},"obitag_bestid":0.9494949494949495,"obitag_bestmatch":"AY227530","obitag_match_count":2,"obitag_rank":"tribe","obitag_similarity_method":"lcs","taxid":"taxon:337730 [Marmotini]@tribe"}
ttagccctaaacataaacattcaataaacaagaatgttcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
>HELIUM_000100422_612GNAAXX:7:30:9942:4495#0/1_sub[28..126] {"count":95,"merged_sample":{"26a_F040644":11,"29a_F260619":84},"obiclean_status":{"26a_F040644":"s","29a_F260619":"h"},"obiclean_weight":{"26a_F040644":12,"29a_F260619":105},"obitag_bestid":0.9595959595959596,"obitag_bestmatch":"AC187326","obitag_match_count":1,"obitag_rank":"subspecies","obitag_similarity_method":"lcs","taxid":"taxon:9615 [Canis lupus familiaris]@subspecies"}
ttagccctaaacataagctattccataacaaaataattcgccagagaactactagcaaca
gattaaacctcaaaggacttggcagtgctttatacccct
>HELIUM_000100422_612GNAAXX:7:51:16702:19393#0/1_sub[28..127] {"count":12004,"merged_sample":{"15a_F730814":7465,"29a_F260619":4539},"obiclean_status":{"15a_F730814":"h","29a_F260619":"h"},"obiclean_weight":{"15a_F730814":8822,"29a_F260619":5789},"obitag_bestid":1,"obitag_bestmatch":"AJ885202","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127] {"count":319,"merged_sample":{"29a_F260619":319},"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":376},"obitag_bestid":1,"obitag_bestmatch":"AJ972683","obitag_match_count":1,"obitag_rank":"species","obitag_similarity_method":"lcs","taxid":"taxon:9858 [Capreolus capreolus]@species"}
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
agcttaaaactcaaaggacttggcggtgctttataccctt
>HELIUM_000100422_612GNAAXX:7:50:10637:6527#0/1_sub[28..126] {"count":366,"merged_sample":{"13a_F730603":13,"15a_F730814":5,"26a_F040644":347,"29a_F260619":1},"obiclean_status":{"13a_F730603":"s","15a_F730814":"s","26a_F040644":"h","29a_F260619":"s"},"obiclean_weight":{"13a_F730603":17,"15a_F730814":5,"26a_F040644":468,"29a_F260619":1},"obitag_bestid":1,"obitag_bestmatch":"AB048590","obitag_match_count":1,"obitag_rank":"genus","obitag_similarity_method":"lcs","taxid":"taxon:9611 [Canis]@genus"}
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
gcttaaaactcaaaggacttggcggtgctttatatccct
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