Add options to startup script
This commit is contained in:
Eric Coissac
4
.gitignore
vendored
4
.gitignore
vendored
@@ -4,6 +4,7 @@
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/jupyterhub_volumes/jupyterhub
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/jupyterhub_volumes/jupyterhub
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/jupyterhub_volumes/caddy
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/jupyterhub_volumes/caddy
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/jupyterhub_volumes/course/data/Genbank
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/jupyterhub_volumes/course/data/Genbank
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/jupyterhub_volumes/web/
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/**/.DS_Store
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/**/.DS_Store
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/web_src/**/*.RData
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/web_src/**/*.RData
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/web_src/**/*.pdf
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/web_src/**/*.pdf
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@@ -14,4 +15,5 @@
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*.log
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*.log
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ncbitaxo_*
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ncbitaxo_*
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Readme_files
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Readme_files
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Readme.html
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Readme.html
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tmp.*
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19
Readme.md
19
Readme.md
@@ -1,4 +1,4 @@
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# JupyterHub Configuration with OrbStack on Mac (all in Docker)
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# OBIJupyterHub - the DNA Metabarcoding Learning Server
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## Intended use
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## Intended use
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@@ -32,6 +32,14 @@ python3 --version
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- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
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- renders the Quarto site from `web_src/`, generates PDF galleries and `pages.json`, and copies everything into `jupyterhub_volumes/web/`
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- runs `docker-compose up -d --remove-orphans`
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- runs `docker-compose up -d --remove-orphans`
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You can tailor what it does with a few flags:
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- `--no-build` (or `--offline`): skip Docker image builds and reuse existing images (useful when offline).
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- `--force-rebuild`: rebuild images without cache.
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- `--stop-server`: stop the stack and remove student containers, then exit.
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- `--update-lectures`: rebuild the course website only (no Docker stop/start).
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- `--build-obidoc`: force rebuilding the obidoc documentation (auto-built if empty; skipped in offline mode).
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## Installation and first run
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## Installation and first run
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1) Clone the project:
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1) Clone the project:
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@@ -78,9 +86,14 @@ OBIJupyterHub
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docker-compose down
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docker-compose down
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```
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```
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### Operating the stack (with one command)
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### Operating the stack (one command, a few options)
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- Start or rebuild at any time with `./start-jupyterhub.sh` from the project root. It rebuilds images, regenerates the website, and starts the stack.
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- Start or rebuild: `./start-jupyterhub.sh` (rebuilds images, regenerates the website, starts the stack).
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- Start without rebuilding images (offline): `./start-jupyterhub.sh --no-build`
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- Force rebuild without cache: `./start-jupyterhub.sh --force-rebuild`
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- Stop only: `./start-jupyterhub.sh --stop-server`
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- Rebuild website only (no Docker stop/start): `./start-jupyterhub.sh --update-lectures`
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- Rebuild obidoc docs: `./start-jupyterhub.sh --build-obidoc` (also builds automatically if `jupyterhub_volumes/web/obidoc` is empty; skipped in offline mode)
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- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
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- Access at `http://localhost:8888` (students: any username / password `metabar2025`; admin: `admin` / `admin2025`).
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- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
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- Check logs from `obijupyterhub/` with `docker-compose logs -f jupyterhub`.
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- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.
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- Stop with `docker-compose down` (from `obijupyterhub/`). Rerun `./start-jupyterhub.sh` to start again or after config changes.
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3
jupyterhub_volumes/web/.gitignore
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3
jupyterhub_volumes/web/.gitignore
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/.quarto/
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/.quarto/
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**/*.quarto_ipynb
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**/*.quarto_ipynb
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/pages/
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/pages/
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/obidoc/
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@@ -1,56 +0,0 @@
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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="UTF-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<meta name="description" content="">
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<meta name="theme-color" media="(prefers-color-scheme: light)" content="#ffffff">
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<meta name="theme-color" media="(prefers-color-scheme: dark)" content="#343a40">
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<meta name="color-scheme" content="light dark"><meta property="og:url" content="http://metabar:8888/obidoc/404.html">
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<meta property="og:site_name" content="OBITools4 documentation">
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<meta property="og:title" content="404 Page not found">
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<meta property="og:locale" content="en_us">
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<meta property="og:type" content="website">
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<title>404 Page not found | OBITools4 documentation</title>
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<link rel="icon" href="/obidoc/favicon.png" >
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<link rel="manifest" href="/obidoc/manifest.json">
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<link rel="canonical" href="http://metabar:8888/obidoc/404.html">
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<link rel="stylesheet" href="/obidoc/book.min.5fd7b8e2d1c0ae15da279c52ff32731130386f71b58f011468f20d0056fe6b78.css" integrity="sha256-X9e44tHArhXaJ5xS/zJzETA4b3G1jwEUaPINAFb+a3g=" crossorigin="anonymous">
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<script defer src="/obidoc/fuse.min.js"></script>
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<script defer src="/obidoc/en.search.min.4da51bdd2d833922fdbc0e19df517221387fc625ffb68ee140d605b3c5b68058.js" integrity="sha256-TaUb3S2DOSL9vA4Z31FyITh/xiX/to7hQNYFs8W2gFg=" crossorigin="anonymous"></script>
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<script defer src="/obidoc/sw.min.32af8eafce4180aa1c5dea66d99fb26ba9043ea7c7a4c706138c91d9051b285e.js" integrity="sha256-Mq+Or85BgKocXepm2Z+ya6kEPqfHpMcGE4yR2QUbKF4=" crossorigin="anonymous"></script>
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<!--
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Made with Book Theme
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https://github.com/alex-shpak/hugo-book
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-->
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<link rel="stylesheet" type="text/css" href="http://metabar:8888/obidoc/hugo-cite.css" />
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<style>
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.not-found {
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text-align: center;
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}
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.not-found h1 {
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margin: .25em 0 0 0;
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opacity: .25;
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font-size: 40vmin;
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}
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</style>
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</head>
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<body>
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<main class="flex justify-center not-found">
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<div>
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<h1>404</h1>
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<h2>Page Not Found</h2>
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<h3>
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<a href="/obidoc/">OBITools4 documentation</a>
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</h3>
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</div>
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</main>
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</body>
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</html>
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Categories on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/categories/</link>
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<description>Recent content in Categories on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<atom:link href="http://metabar:8888/obidoc/categories/index.xml" rel="self" type="application/rss+xml" />
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</channel>
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</rss>
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<!DOCTYPE html>
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<html lang="en-us">
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<head>
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<title>http://metabar:8888/obidoc/categories/</title>
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<link rel="canonical" href="http://metabar:8888/obidoc/categories/">
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<meta charset="utf-8">
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<meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/categories/">
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</head>
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</html>
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Commands on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/commands/</link>
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<description>Recent content in Commands on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<atom:link href="http://metabar:8888/obidoc/commands/index.xml" rel="self" type="application/rss+xml" />
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</channel>
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</rss>
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<!DOCTYPE html>
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<html lang="en-us">
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<head>
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<title>http://metabar:8888/obidoc/commands/</title>
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<link rel="canonical" href="http://metabar:8888/obidoc/commands/">
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<meta charset="utf-8">
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<meta http-equiv="refresh" content="0; url=http://metabar:8888/obidoc/commands/">
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</head>
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</html>
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.admonition{margin:1rem 0;border-radius:4px;box-shadow:0 1px 3px rgba(0,0,0,0.12);transition:all 0.3s ease}.admonition-header{padding:0.5rem 1rem;display:flex;align-items:center;font-weight:600;border-bottom:1px solid rgba(0,0,0,0.1);font-size:1.1rem;border-radius:4px 4px 0 0}.admonition-header svg{width:1.1em;height:1.1em;margin-right:0.5rem;fill:currentColor}.admonition-content{padding:1rem;background-color:#fff;border-radius:0 0 4px 4px;color:#000;transition:background-color 0.3s ease, color 0.3s ease}.admonition-content p{margin:0 0 0.5rem 0}.admonition-content p:last-child{margin-bottom:0}.admonition-content ul,.admonition-content ol{margin:0 0 0.5rem 0;padding-left:1.2rem}.admonition-content ul:last-child,.admonition-content ol:last-child{margin-bottom:0}.admonition-content blockquote{margin:0 0 0.5rem 0;padding-left:1rem;border-left:3px solid #e0e0e0}.admonition-content blockquote:last-child{margin-bottom:0}.admonition-content code{background-color:#f5f5f5;color:#24292e;padding:0.2em 0.4em;border-radius:3px;font-size:0.9em}@media (prefers-color-scheme: dark){.admonition-content{background-color:#1D1E20;color:#e6e6e6}.admonition-content code{background-color:#313244;color:#cdd6f4}.admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}}body.dark .admonition-content{background-color:#1D1E20;color:#e6e6e6}body.dark .admonition-content code{background-color:#313244;color:#cdd6f4}body.dark .admonition-content blockquote{border-left-color:#45475a;color:#cdd6f4}.admonition.abstract{background:transparent;border-left:4px solid #209fb5}.admonition.abstract .admonition-header{background:rgba(32,159,181,0.1);color:#209fb5}.admonition.caution{background:transparent;border-left:4px solid #e64553}.admonition.caution .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.code{background:transparent;border-left:4px solid #7287fd}.admonition.code .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.conclusion{background:transparent;border-left:4px solid #dd7878}.admonition.conclusion .admonition-header{background:rgba(221,120,120,0.1);color:#dd7878}.admonition.danger{background:transparent;border-left:4px solid #fe640b}.admonition.danger .admonition-header{background:rgba(254,100,11,0.1);color:#fe640b}.admonition.error{background:transparent;border-left:4px solid #d20f39}.admonition.error .admonition-header{background:rgba(210,15,57,0.1);color:#d20f39}.admonition.example{background:transparent;border-left:4px solid #dc8a78}.admonition.example .admonition-header{background:rgba(220,138,120,0.1);color:#dc8a78}.admonition.experiment{background:transparent;border-left:4px solid #51bb2a}.admonition.experiment .admonition-header{background:rgba(81,187,42,0.1);color:#51bb2a}.admonition.goal{background:transparent;border-left:4px solid #e64553}.admonition.goal .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.idea{background:transparent;border-left:4px solid #df8e1d}.admonition.idea .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}.admonition.important{background:transparent;border-left:4px solid #7D4DDA}.admonition.important .admonition-header{background:rgba(125,77,218,0.1);color:#7D4DDA}.admonition.info{background:transparent;border-left:4px solid #04a5e5}.admonition.info .admonition-header{background:rgba(4,165,229,0.1);color:#04a5e5}.admonition.memo{background:transparent;border-left:4px solid #e64553}.admonition.memo .admonition-header{background:rgba(230,69,83,0.1);color:#e64553}.admonition.note{background:transparent;border-left:4px solid #096ae1}.admonition.note .admonition-header{background:rgba(9,106,225,0.1);color:#096ae1}.admonition.notify{background:transparent;border-left:4px solid #0d48bd}.admonition.notify .admonition-header{background:rgba(13,72,189,0.1);color:#0d48bd}.admonition.question{background:transparent;border-left:4px solid #179299}.admonition.question .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.quote{background:transparent;border-left:4px solid #7287fd}.admonition.quote .admonition-header{background:rgba(114,135,253,0.1);color:#7287fd}.admonition.success{background:transparent;border-left:4px solid #40a02b}.admonition.success .admonition-header{background:rgba(64,160,43,0.1);color:#40a02b}.admonition.task{background:transparent;border-left:4px solid #8839ef}.admonition.task .admonition-header{background:rgba(136,57,239,0.1);color:#8839ef}.admonition.tip{background:transparent;border-left:4px solid #179299}.admonition.tip .admonition-header{background:rgba(23,146,153,0.1);color:#179299}.admonition.warning{background:transparent;border-left:4px solid #df8e1d}.admonition.warning .admonition-header{background:rgba(223,142,29,0.1);color:#df8e1d}
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Advanced tools on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/docs/commands/advanced/</link>
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<description>Recent content in Advanced tools on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<lastBuildDate></lastBuildDate>
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<atom:link href="http://metabar:8888/obidoc/docs/commands/advanced/index.xml" rel="self" type="application/rss+xml" />
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</channel>
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</rss>
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Sequence alignments on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/docs/commands/alignments/</link>
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<description>Recent content in Sequence alignments on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<lastBuildDate></lastBuildDate>
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<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/index.xml" rel="self" type="application/rss+xml" />
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</channel>
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</rss>
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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<channel>
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<title>Exact alignment on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/</link>
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<description>Recent content in Exact alignment on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/exact-alignment/index.xml" rel="self" type="application/rss+xml" />
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</channel>
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</rss>
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---
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title: "Untitled"
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format: html
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editor: visual
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---
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```{r}
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library(tidyverse)
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library(plotly)
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library(matrixStats)
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```
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```{r}
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log_sum_exp <- function(a,b) {
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m <- map2_dbl(a,b,max)
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m + log(exp(a-m)+exp(b-m))
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}
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```
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$$
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\log(1 - e^b) = \log\left(-e^{(1-b)}\right)
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$$
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```{r}
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log1m_exp <- function(b) {
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if (any(b >= 0)) {
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stop(glue::glue("b must be negative (b={b})"))
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}
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return(log(-expm1(b))) # expm1(b) = exp(b) - 1, pour éviter les erreurs d'arrondi
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}
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```
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|
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$$
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|
||||||
\log(e^a - e^b) = a + \log(1 - e^{b-a})
|
|
||||||
$$
|
|
||||||
|
|
||||||
```{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<75>rieur <20> 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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|||||||
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|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>The FASTA-like alignment on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/</link>
|
|
||||||
<description>Recent content in The FASTA-like alignment on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/alignments/obipairing/fasta-like/index.xml" rel="self" type="application/rss+xml" />
|
|
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|
||||||
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|
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|||||||
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|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Basics on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/basics/</link>
|
|
||||||
<description>Recent content in Basics on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/basics/index.xml" rel="self" type="application/rss+xml" />
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|
|
||||||
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|
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|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Demultiplexing samples on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/demultiplexing/</link>
|
|
||||||
<description>Recent content in Demultiplexing samples on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/demultiplexing/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Experimentals on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/experimental/</link>
|
|
||||||
<description>Recent content in Experimentals on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/experimental/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>The OBITools4 commands on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/</link>
|
|
||||||
<description>Recent content in The OBITools4 commands on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate>Fri, 04 Oct 2024 17:16:03 +0200</lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
<item>
|
|
||||||
<title>Glossary of tags</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/tags/</link>
|
|
||||||
<pubDate>Fri, 04 Oct 2024 17:16:03 +0200</pubDate>
|
|
||||||
<guid>http://metabar:8888/obidoc/docs/commands/tags/</guid>
|
|
||||||
<description><h1 id="glossary-of-tags">
 Glossary of tags
 <a class="anchor" href="#glossary-of-tags">#</a>
</h1>
<h3 id="--d--">
 - D -
 <a class="anchor" href="#--d--">#</a>
</h3>
<ul>
<li>
<p><strong>definition</strong> :</p>
<blockquote>
<p>text information about the sequence present in the original sequence file.</p>
</blockquote>
</li>
<li>
<p><strong>direction</strong> :</p>
<blockquote>
<p>set to “forward” if the original sequence did not need to be reverse-complemented to be processed, set to “reverse” otherwise.
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
</ul>
<h3 id="--f--">
 - F -
 <a class="anchor" href="#--f--">#</a>
</h3>
<ul>
<li>
<p><strong>forward_error</strong> :</p>
<blockquote>
<p>Number of mismatch between forward primer and priming site
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_match</strong> :</p>
<blockquote>
<p>Forward primer priming site sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p>
</blockquote>
</li>
<li>
<p><strong>forward_primer</strong> :</p>
<blockquote>
<p>Forward primer sequence
(
 <a href="http://metabar:8888/obidoc/obitools/obipcr/">obipcr</a>)</p></description>
|
|
||||||
</item>
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Shared command options on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/options/</link>
|
|
||||||
<description>Recent content in Shared command options on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/options/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
@@ -1,6 +0,0 @@
|
|||||||
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
|
||||||
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
|
||||||
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
|
|
||||||
agcttaaaactcaaaggacctggcagttctttatatccct
|
|
||||||
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Others on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/others/</link>
|
|
||||||
<description>Recent content in Others on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/others/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
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File diff suppressed because it is too large
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@@ -1,12 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Taxonomy on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/commands/taxonomy/</link>
|
|
||||||
<description>Recent content in Taxonomy on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/commands/taxonomy/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
@@ -1,604 +0,0 @@
|
|||||||
#!/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'])
|
|
||||||
|
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -1,11 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Designing new barcodes on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/cookbook/ecoprimers/</link>
|
|
||||||
<description>Recent content in Designing new barcodes on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/ecoprimers/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
Binary file not shown.
|
Before Width: | Height: | Size: 168 KiB |
@@ -1,103 +0,0 @@
|
|||||||
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 -
|
|
||||||
File diff suppressed because it is too large
Load Diff
@@ -1,11 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<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>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/illumina/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
Binary file not shown.
|
Before Width: | Height: | Size: 16 KiB |
Binary file not shown.
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1,26 +0,0 @@
|
|||||||
>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
|
|
||||||
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
File diff suppressed because it is too large
Load Diff
@@ -1,24 +0,0 @@
|
|||||||
>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}}
|
|
||||||
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
|
|
||||||
@@ -1,329 +0,0 @@
|
|||||||
>HELIUM_000100422_612GNAAXX:7:56:19300:10949#0/1_sub[28..127] {"count":37,"merged_sample":{"29a_F260619":37},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":43}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactagcggcaac
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:63:4595:15643#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":4}}
|
|
||||||
ttagccctaaacataagctattccataacaaaataattcgccagagtactaccggcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:8807:7823#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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtcataccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:108:19171:11413#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:8:6794:4925#0/1_sub[28..127]":"(t)->(g)@38"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaagtagtcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:44:5008:2115#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}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:53:16956:10563#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":4}}
|
|
||||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:54:10323:7022#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
|
||||||
ttagccctaaacacaaataattatataaacaaaactattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:45:7460:13396#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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatgcccgt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:58:8409:9911#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>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:7:100:18844:15930#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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaagcgcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:29:9723:20435#0/1_sub[28..127] {"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":4}}
|
|
||||||
ttagccctaaacacaaataattacacaaacaaaattgttcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:43:4660:16319#0/1_sub[28..126] {"count":22,"merged_sample":{"26a_F040644":22},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":42}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:103:11045:3860#0/1_sub[28..127] {"count":4,"merged_sample":{"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s"},"obiclean_weight":{"15a_F730814":4}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaagggcttggcggtgctttatgccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:67:10944:19430#0/1_sub[28..127] {"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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgtcagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacgtggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:56:6962:17278#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":7}}
|
|
||||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:60:13553:20530#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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
atgttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:35:13167:18371#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccggagaactactaggaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:105:1895:7593#0/1_sub[28..127] {"count":11,"merged_sample":{"29a_F260619":11},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":13}}
|
|
||||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
|
||||||
agcttaaaactcaaaggacctggcggtgcttcatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:118:15661:12736#0/1_sub[28..127] {"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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattatccgcaagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:30:8391:13152#0/1_sub[28..127] {"count":17,"merged_sample":{"13a_F730603":17},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":25}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
|
||||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:95:14375:10838#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":5}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcagtgctttatacccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:82:13334:18499#0/1_sub[28..127] {"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":10}}
|
|
||||||
ttagccctaaacacaaataattacacaaacaaaattgttcaccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:108:11272:1128#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}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactactagcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:6016:14767#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":4}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacgtctagcaaca
|
|
||||||
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:7:9:8337:12329#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":6}}
|
|
||||||
ttagccctaaacataaacagtcaataaacaaggatgttcgccagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:15:12854:18952#0/1_sub[28..126] {"count":10,"merged_sample":{"29a_F260619":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":16}}
|
|
||||||
ttagccctaaacataagctattccataacaaaattattcgccagagtactaccggcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:1:4513:20277#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}}
|
|
||||||
ttagccctaaacataaaccattctataacaaaataattcgccagaggactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:57:18237:6765#0/1_sub[28..127] {"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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattatgcgccagagtactgccggcaat
|
|
||||||
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:7:119:8691:15994#0/1_sub[28..127] {"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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcgat
|
|
||||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:6:1739:11421#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgctagagtactactagcaaca
|
|
||||||
gcctgacactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:73:17136:17728#0/1_sub[28..127] {"count":6,"merged_sample":{"13a_F730603":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":7}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaattattcgccagagtactaccggcaac
|
|
||||||
agcccaaaactcaaaggacttggcggtgcttcacaccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:76:9874:3117#0/1_sub[28..127] {"count":9,"merged_sample":{"29a_F260619":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactagcggcaac
|
|
||||||
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:7:18:16679:15889#0/1_sub[28..127] {"count":4,"merged_sample":{"29a_F260619":4},"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}}
|
|
||||||
ttagccctaaacctcaacagttaaatcaacaaaactgctcgccagaacactacgagccac
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:52:6908:8410#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":10}}
|
|
||||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttatacccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:71:13461:7411#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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagaagactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>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:7:47:6989:13864#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"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}}
|
|
||||||
ttagccctaaacataaaccattctataacaaaataattcgccagagaactactagcaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:72:8941:18482#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
|
||||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:25:10818:13742#0/1_sub[28..133] {"count":8,"merged_sample":{"26a_F040644":8},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
|
||||||
ttagccctaaacgtaaactgcaaactattccataataaaataattcgcccaagaactact
|
|
||||||
agcaacagcttaaaactcaaaggacttggtggtgctttctacccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:70:11509:6042#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}}
|
|
||||||
ttagccctaaacacaagaaattaatataacaaaaatattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>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:7:46:4342:17317#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":8}}
|
|
||||||
ttagccctaaacataaatcattctataacaaaataattcgccggagaactactaggaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgccttacgtccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:111:17844:17230#0/1_sub[28..126] {"count":13,"merged_sample":{"26a_F040644":13},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":17}}
|
|
||||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
|
||||||
gcttaaaactcaaaggacgtggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:34:17680:16952#0/1_sub[28..127] {"count":15,"merged_sample":{"13a_F730603":15},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":15}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgcttcacaccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:34:2640:2539#0/1_sub[28..127] {"count":19,"merged_sample":{"29a_F260619":19},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"29a_F260619":"h"},"obiclean_weight":{"29a_F260619":25}}
|
|
||||||
ttagccctaaacacaaataattacacaaacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:71:18891:9661#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"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}}
|
|
||||||
ttagccctaaacataaatcagtctataacaaaataattcgccagagaactactagcaaca
|
|
||||||
gcttaaaactcaaaggacgtggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:26:16553:1613#0/1_sub[77..81] {"count":38,"merged_sample":{"13a_F730603":38},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":38}}
|
|
||||||
caata
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:45:5732:11220#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggtggtgctttctacccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:1:14254:1103#0/1_sub[28..126] {"count":8,"merged_sample":{"26a_F040644":8},"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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:50:17151:20608#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaaaataattcgccagaggactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:96:13203:2879#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":6}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtactaccggcaac
|
|
||||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:78:18041:18996#0/1_sub[28..126] {"count":13,"merged_sample":{"13a_F730603":9,"15a_F730814":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":2,"obiclean_singletoncount":2,"obiclean_status":{"13a_F730603":"s","15a_F730814":"s"},"obiclean_weight":{"13a_F730603":9,"15a_F730814":4}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:80:18387:10166#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:100:14685:15065#0/1_sub[28..127]":"(a)->(t)@24","HELIUM_000100422_612GNAAXX:7:84:14502:1617#0/1_sub[28..127]":"(t)->(g)@71"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"s","29a_F260619":"i"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
|
||||||
ttagccctaaacacaagtaattattataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaacgcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:54:10113:12172#0/1_sub[28..127] {"count":7,"merged_sample":{"15a_F730814":4,"29a_F260619":3},"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":5,"29a_F260619":4}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:97:17822:18365#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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtactgccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatcccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:87:6328:12406#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":8}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcagtgctttatacccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:4611:13145#0/1_sub[28..127] {"count":3,"merged_sample":{"13a_F730603":3},"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}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacgtccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>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:7:78:6346:5817#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":5}}
|
|
||||||
ttagccctaaacacaaataattatataaacaaaattattcgccagagtactaccggcaac
|
|
||||||
agcccaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:15122:17310#0/1_sub[28..127] {"count":2,"merged_sample":{"15a_F730814":1,"29a_F260619":1},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":1,"obiclean_mutation":{"HELIUM_000100422_612GNAAXX:7:94:6384:20392#0/1_sub[28..127]":"(a)->(t)@52"},"obiclean_samplecount":2,"obiclean_singletoncount":1,"obiclean_status":{"15a_F730814":"i","29a_F260619":"s"},"obiclean_weight":{"15a_F730814":1,"29a_F260619":1}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacttcctgcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:27:7695:17738#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:48:15379:13773#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}}
|
|
||||||
ttagccctaaacatagataattttacaacaagaatgttcgccagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:117:16246:17184#0/1_sub[28..127] {"count":5,"merged_sample":{"13a_F730603":5},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"13a_F730603":"s"},"obiclean_weight":{"13a_F730603":10}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:87:11044:6323#0/1_sub[28..126] {"count":69,"merged_sample":{"26a_F040644":69},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"26a_F040644":"h"},"obiclean_weight":{"26a_F040644":84}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:40:12248:18615#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
|
||||||
ttagccctaaacataagctattctataacaaaataattcgccagagaactactagcaaca
|
|
||||||
gcttaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:6470:13562#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}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattattcgccagagtacctccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:72:11850:15705#0/1_sub[28..126] {"count":4,"merged_sample":{"26a_F040644":4},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaata
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:82:8566:4827#0/1_sub[28..126] {"count":6,"merged_sample":{"26a_F040644":6},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":9}}
|
|
||||||
ttagccctaaacataaacattcaataaacaaggatgttcgcaagagtactactagcaatg
|
|
||||||
gcctaaaactcaaaggacttggtggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:43:16297:17399#0/1_sub[28..127] {"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":3}}
|
|
||||||
ttagccctaaacacaagtaattaatataacaaaattgttcaccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:15117:2564#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}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagagtacctccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:90:4058:17862#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":5}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaaactattcgccagaggactactagcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttataccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:43:13909:1377#0/1_sub[28..126] {"count":10,"merged_sample":{"26a_F040644":10},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":14}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactagcaatg
|
|
||||||
gcctaaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:36:3584:21256#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}}
|
|
||||||
ctagccttaaacacaaatagttatgcaaacaaagctattcgccagagtactaccggcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatgccctt
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:80:13357:2959#0/1_sub[74..81] {"count":12,"merged_sample":{"29a_F260619":12},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"29a_F260619":"s"},"obiclean_weight":{"29a_F260619":12}}
|
|
||||||
ccgatagg
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:70:8097:4516#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}}
|
|
||||||
ttagccctaaacataaacattcaagaaacaagaatgttcaccagagtactactagcaatg
|
|
||||||
gcctaaaactcaaaggacttggcagtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:7:8746:5790#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtacctctagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:8:9165:18915#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}}
|
|
||||||
ttagccctaaacataaacattcaataaacaagaatgttcgccagagtactactatgaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:85:7323:6139#0/1_sub[28..126] {"count":9,"merged_sample":{"26a_F040644":9},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":16}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagaggactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttacatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:23:6103:3418#0/1_sub[28..126] {"count":3,"merged_sample":{"26a_F040644":3},"obiclean_head":true,"obiclean_headcount":0,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":1,"obiclean_status":{"26a_F040644":"s"},"obiclean_weight":{"26a_F040644":4}}
|
|
||||||
ttagccctaaacatagataattttacaacaaaataattcgccagagtactactagcaaca
|
|
||||||
gcctgaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>HELIUM_000100422_612GNAAXX:7:107:2103:10677#0/1_sub[28..127] {"count":20,"merged_sample":{"13a_F730603":20},"obiclean_head":true,"obiclean_headcount":1,"obiclean_internalcount":0,"obiclean_samplecount":1,"obiclean_singletoncount":0,"obiclean_status":{"13a_F730603":"h"},"obiclean_weight":{"13a_F730603":22}}
|
|
||||||
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
|
|
||||||
@@ -1,24 +0,0 @@
|
|||||||
>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
|
|
||||||
@@ -1,24 +0,0 @@
|
|||||||
>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
|
|
||||||
@@ -1,9 +0,0 @@
|
|||||||
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
|
|
||||||
|
@@ -1,6 +0,0 @@
|
|||||||
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
|
|
||||||
|
|
||||||
|
@@ -1,24 +0,0 @@
|
|||||||
>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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|
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|
|||||||
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|
|
||||||
@param,primer_mismatches,2
|
|
||||||
@param,indels,false
|
|
||||||
experiment,sample,sample_tag,forward_primer,reverse_primer
|
|
||||||
wolf_diet,13a_F730603,aattaac,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
|
||||||
wolf_diet,15a_F730814,gaagtag,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
|
||||||
wolf_diet,26a_F040644,gaatatc,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
|
||||||
wolf_diet,29a_F260619,gcctcct,TTAGATACCCCACTATGC,TAGAACAGGCTCCTCTAG
|
|
||||||
|
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|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Cookbook on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/cookbook/</link>
|
|
||||||
<description>Recent content in Cookbook on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
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|
|
||||||
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|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
@@ -1,102 +0,0 @@
|
|||||||
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 : $(GBDIV_ALL)
|
|
||||||
|
|
||||||
FORCE:
|
|
||||||
|
|
||||||
.PHONY: all directories depends taxonomy fasta_files FORCE
|
|
||||||
|
|
||||||
depends: directories Release_$(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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|
|||||||
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|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Prepare a local copy of Genbank on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/cookbook/local_genbank/</link>
|
|
||||||
<description>Recent content in Prepare a local copy of Genbank on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/local_genbank/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
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|
|
||||||
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|
||||||
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|||||||
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|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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|
||||||
<channel>
|
|
||||||
<title>Oxford Nanopore data analysis on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/cookbook/minion/</link>
|
|
||||||
<description>Recent content in Oxford Nanopore data analysis on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/minion/index.xml" rel="self" type="application/rss+xml" />
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|
||||||
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|
||||||
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|
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Build a reference database on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/cookbook/reference_db/</link>
|
|
||||||
<description>Recent content in Build a reference database on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate></lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/cookbook/reference_db/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
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|
|
||||||
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|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>File formats on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/</link>
|
|
||||||
<description>Recent content in File formats on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
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@@ -1,11 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>Annotation of sequences on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/</link>
|
|
||||||
<description>Recent content in Annotation of sequences on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/annotations/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
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@@ -1,11 +0,0 @@
|
|||||||
<?xml version="1.0" encoding="utf-8" standalone="yes"?>
|
|
||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
|
|
||||||
<channel>
|
|
||||||
<title>CSV format on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/</link>
|
|
||||||
<description>Recent content in CSV format on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/sequence_files/csv/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
</channel>
|
|
||||||
</rss>
|
|
||||||
@@ -1,6 +0,0 @@
|
|||||||
>AB061527 {"count":1,"definition":"Sorex unguiculatus mitochondrial NA, complete genome.","family_name":"Soricidae","family_taxid":9376,"genus_name":"Sorex","genus_taxid":9379,"obicleandb_level":"family","obicleandb_trusted":2.2137847111025621e-13,"species_name":"Sorex unguiculatus","species_taxid":62275,"taxid":62275}
|
|
||||||
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
|
|
||||||
agcttaaaactcaaaggacttggcggtgctttatatccct
|
|
||||||
>AL355887 {"count":2,"definition":"Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.","family_name":"Hominidae","family_taxid":9604,"genus_name":"Homo","genus_taxid":9605,"obicleandb_level":"genus","obicleandb_trusted":0,"species_name":"Homo sapiens","species_taxid":9606,"taxid":9606}
|
|
||||||
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
|
|
||||||
agcttaaaactcaaaggacctggcagttctttatatccct
|
|
||||||
@@ -1,8 +0,0 @@
|
|||||||
@HELIUM_000100422_612GNAAXX:7:108:5640:3823#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(T:26)->(G:13)":62,"(T:34)->(G:18)":48},"score":484,"score_norm":0.968,"seq_a_single":46,"seq_ab_match":60,"seq_b_single":46}
|
|
||||||
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattgttcgccagagtactaccggcaatagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
|
||||||
+
|
|
||||||
CCCCCCCBCCCCCCCCCCCCCCCCCCCCCCBCCCCCBCCCCCCC<CcCccbe[`F`accXV<TA\RYU\\ee_e[XZ[XEEEEEEEEEE?EEEEEEEEEEDEEEEEEECCCCCCCCCCCCCCCCCCCCCCCACCCCCACCCCCCCCCCCCCCCC
|
|
||||||
@HELIUM_000100422_612GNAAXX:7:97:14311:19299#0/1 {"ali_dir":"left","ali_length":62,"mode":"alignment","pairing_mismatches":{"(A:02)->(G:30)":104,"(A:34)->(G:14)":64,"(C:02)->(A:30)":86,"(C:02)->(T:20)":108,"(C:27)->(G:32)":83,"(C:34)->(G:18)":57,"(T:02)->(G:26)":87,"(T:22)->(G:14)":66,"(T:29)->(G:11)":62,"(T:32)->(G:30)":48},"score":283,"score_norm":0.839,"seq_a_single":46,"seq_ab_match":52,"seq_b_single":46}
|
|
||||||
ccgcctcctttagataccccactatgcttagccctaaacacaagtaattaatataacaaaattattcgccagagtactaccggcaagagcttaaaactcaaaggacttggcggtgctttatacccttctagaggagcctgttctaaggaggcgg
|
|
||||||
+
|
|
||||||
CCCCCCCCCCCCCCCCCCCCCCCBBCCC?BCCCCCBC?CCCC@@;AVA`cWeb_TYC\UIN?IDP8QJMKRPVGLQAFPPc`AbAFB5A4>AAA56A><>8>>F@A><8??@BB+<?;?C@9CCCCCC<CC=CCCCCCCCCBC?CBCCCCC@CC
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<channel>
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<title>Sequence file formats on OBITools4 documentation</title>
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<link>http://metabar:8888/obidoc/docs/file_format/sequence_files/</link>
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<description>Recent content in Sequence file formats on OBITools4 documentation</description>
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<generator>Hugo</generator>
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<language>en-us</language>
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|
|||||||
taxid,parent,taxonomic_rank,scientific_name
|
|
||||||
taxon:1 [root]@no rank,taxon:1 [root]@no rank,no rank,root
|
|
||||||
taxon:131567 [cellular organisms]@no rank,taxon:1 [root]@no rank,no rank,cellular organisms
|
|
||||||
taxon:2759 [Eukaryota]@superkingdom,taxon:131567 [cellular organisms]@no rank,superkingdom,Eukaryota
|
|
||||||
taxon:33090 [Viridiplantae]@kingdom,taxon:2759 [Eukaryota]@superkingdom,kingdom,Viridiplantae
|
|
||||||
taxon:35493 [Streptophyta]@phylum,taxon:33090 [Viridiplantae]@kingdom,phylum,Streptophyta
|
|
||||||
taxon:131221 [Streptophytina]@subphylum,taxon:35493 [Streptophyta]@phylum,subphylum,Streptophytina
|
|
||||||
taxon:3193 [Embryophyta]@clade,taxon:131221 [Streptophytina]@subphylum,clade,Embryophyta
|
|
||||||
taxon:58023 [Tracheophyta]@clade,taxon:3193 [Embryophyta]@clade,clade,Tracheophyta
|
|
||||||
taxon:78536 [Euphyllophyta]@clade,taxon:58023 [Tracheophyta]@clade,clade,Euphyllophyta
|
|
||||||
taxon:58024 [Spermatophyta]@clade,taxon:78536 [Euphyllophyta]@clade,clade,Spermatophyta
|
|
||||||
taxon:3398 [Magnoliopsida]@class,taxon:58024 [Spermatophyta]@clade,class,Magnoliopsida
|
|
||||||
taxon:1437183 [Mesangiospermae]@clade,taxon:3398 [Magnoliopsida]@class,clade,Mesangiospermae
|
|
||||||
taxon:71240 [eudicotyledons]@clade,taxon:1437183 [Mesangiospermae]@clade,clade,eudicotyledons
|
|
||||||
taxon:91827 [Gunneridae]@clade,taxon:71240 [eudicotyledons]@clade,clade,Gunneridae
|
|
||||||
taxon:1437201 [Pentapetalae]@clade,taxon:91827 [Gunneridae]@clade,clade,Pentapetalae
|
|
||||||
taxon:71275 [rosids]@clade,taxon:1437201 [Pentapetalae]@clade,clade,rosids
|
|
||||||
taxon:91835 [fabids]@clade,taxon:71275 [rosids]@clade,clade,fabids
|
|
||||||
taxon:3502 [Fagales]@order,taxon:91835 [fabids]@clade,order,Fagales
|
|
||||||
taxon:3514 [Betulaceae]@family,taxon:3502 [Fagales]@order,family,Betulaceae
|
|
||||||
taxon:3504 [Betula]@genus,taxon:3514 [Betulaceae]@family,genus,Betula
|
|
||||||
taxon:1685988 [Betula murrayana]@species,taxon:3504 [Betula]@genus,species,Betula murrayana
|
|
||||||
taxon:361422 [Betula ovalifolia]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia
|
|
||||||
taxon:1685972 [Betula x caerulea]@species,taxon:3504 [Betula]@genus,species,Betula x caerulea
|
|
||||||
taxon:216986 [Betula schmidtii]@species,taxon:3504 [Betula]@genus,species,Betula schmidtii
|
|
||||||
taxon:312791 [Betula michauxii]@species,taxon:3504 [Betula]@genus,species,Betula michauxii
|
|
||||||
taxon:3015411 [Betula pamirica]@species,taxon:3504 [Betula]@genus,species,Betula pamirica
|
|
||||||
taxon:312792 [Betula raddeana]@species,taxon:3504 [Betula]@genus,species,Betula raddeana
|
|
||||||
taxon:216991 [Betula humilis]@species,taxon:3504 [Betula]@genus,species,Betula humilis
|
|
||||||
taxon:2218489 [Betula ovalifolia x Betula ermanii]@species,taxon:3504 [Betula]@genus,species,Betula ovalifolia x Betula ermanii
|
|
||||||
|
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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|
||||||
<channel>
|
|
||||||
<title>CSV formatted taxdump on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/csv_taxdump/</link>
|
|
||||||
<description>Recent content in CSV formatted taxdump on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
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|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/taxonomy_file/csv_taxdump/index.xml" rel="self" type="application/rss+xml" />
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<channel>
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||||||
<title>Taxonomy file formats on OBITools4 documentation</title>
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|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/</link>
|
|
||||||
<description>Recent content in Taxonomy file formats on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
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|
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<language>en-us</language>
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|
||||||
<channel>
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|
||||||
<title>NCBI taxdump on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/</link>
|
|
||||||
<description>Recent content in NCBI taxdump on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
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|
||||||
<language>en-us</language>
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|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/file_format/taxonomy_file/ncbi_taxdump/index.xml" rel="self" type="application/rss+xml" />
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||||||
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<?xml version="1.0" encoding="utf-8" standalone="yes"?>
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||||||
<rss version="2.0" xmlns:atom="http://www.w3.org/2005/Atom">
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|
||||||
<channel>
|
|
||||||
<title>Docs on OBITools4 documentation</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/</link>
|
|
||||||
<description>Recent content in Docs on OBITools4 documentation</description>
|
|
||||||
<generator>Hugo</generator>
|
|
||||||
<language>en-us</language>
|
|
||||||
<lastBuildDate>Mon, 01 Jan 0001 00:00:00 +0000</lastBuildDate>
|
|
||||||
<atom:link href="http://metabar:8888/obidoc/docs/index.xml" rel="self" type="application/rss+xml" />
|
|
||||||
<item>
|
|
||||||
<title>About</title>
|
|
||||||
<link>http://metabar:8888/obidoc/docs/about/</link>
|
|
||||||
<pubDate>Mon, 01 Jan 0001 00:00:00 +0000</pubDate>
|
|
||||||
<guid>http://metabar:8888/obidoc/docs/about/</guid>
|
|
||||||
<description><h2 id="what-are-obitools4">
 What are OBITools4?
 <a class="anchor" href="#what-are-obitools4">#</a>
</h2>
<p>The development of <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 began at 
 <a href="https://leca.osug.fr"><abbr title="LECA: Laboratoire d&#39;écologie Alpine - Laboratory for Alpine Ecology">LECA</abbr>
 
 </a> (
 <a href="https://www.univ-grenoble-alpes.fr/">University of Grenoble</a>) in the early 2000s, at the same time as the development of DNA metabarcoding methods in the same laboratory. The idea behind the OBITools project was to provide a set of UNIX command-line tools that mimic standard UNIX shell commands such as <code>grep</code>, <code>uniq</code> or <code>wc</code>, but which work on DNA sequence files. Unlike standard UNIX tools, where the processing unit is a line of text, with OBITools the processing unit is a sequence record. In addition, some commands implementing algorithms specific to the processing of DNA metabarcoding data have been added, making <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
 one of the sequence processing tools widely used on UNIX-like systems, suitable for the analysis of DNA metabarcoding data.</p></description>
|
|
||||||
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|
||||||
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|
||||||
</rss>
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|
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Reference in New Issue
Block a user