repos: 209590345
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| id | node_id | name | full_name | private | owner | html_url | description | fork | created_at | updated_at | pushed_at | homepage | size | stargazers_count | watchers_count | language | has_issues | has_projects | has_downloads | has_wiki | has_pages | forks_count | archived | disabled | open_issues_count | license | topics | forks | open_issues | watchers | default_branch | permissions | temp_clone_token | organization | network_count | subscribers_count | readme | readme_html | allow_forking | visibility | is_template | template_repository | web_commit_signoff_required | has_discussions |
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| 209590345 | MDEwOlJlcG9zaXRvcnkyMDk1OTAzNDU= | genome-to-sqlite | dogsheep/genome-to-sqlite | 0 | 53015001 | https://github.com/dogsheep/genome-to-sqlite | Import your genome into a SQLite database | 0 | 2019-09-19T15:38:39Z | 2021-01-18T19:39:48Z | 2019-09-19T15:41:17Z | 9 | 13 | 13 | Python | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 0 | 2 | apache-2.0 | ["genetics", "sqlite", "23andme", "personal-analytics", "datasette", "dogsheep", "datasette-io", "datasette-tool"] | 0 | 2 | 13 | master | {"admin": false, "push": false, "pull": false} | 53015001 | 0 | 2 | # genome-to-sqlite [](https://pypi.org/project/genome-to-sqlite/) [](https://circleci.com/gh/dogsheep/genome-to-sqlite) [](https://github.com/dogsheep/genome-to-sqlite/blob/master/LICENSE) Import your genome into a SQLite database. ## How to install $ pip install genome-to-sqlite ## How to use First, export your genome. This tool has only been tested against 23andMe so far. You can request an export of your genome from https://you.23andme.com/tools/data/download/ Now you can convert the resulting `export.zip` file to SQLite like so: $ genome-to-sqlite export.zip genome.db A progress bar will be displayed. You can disable this using `--silent`. ``` Importing genome [#----------------] 5% 00:01:33 ``` You can explore the resulting data using [Datasette](https://datasette.readthedocs.io/) like this: $ datasette genome.db --config facet_time_limit_ms:1000 Bumping up the facet time limit is useful in order to enable faceting by chromosome: http://127.0.0.1:8001/genome/genome?_facet=chromosome&_sort=position | <div id="readme" class="md" data-path="README.md"><article class="markdown-body entry-content container-lg" itemprop="text"><h1><a id="user-content-genome-to-sqlite" class="anchor" aria-hidden="true" href="#user-content-genome-to-sqlite"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.775 3.275a.75.75 0 001.06 1.06l1.25-1.25a2 2 0 112.83 2.83l-2.5 2.5a2 2 0 01-2.83 0 .75.75 0 00-1.06 1.06 3.5 3.5 0 004.95 0l2.5-2.5a3.5 3.5 0 00-4.95-4.95l-1.25 1.25zm-4.69 9.64a2 2 0 010-2.83l2.5-2.5a2 2 0 012.83 0 .75.75 0 001.06-1.06 3.5 3.5 0 00-4.95 0l-2.5 2.5a3.5 3.5 0 004.95 4.95l1.25-1.25a.75.75 0 00-1.06-1.06l-1.25 1.25a2 2 0 01-2.83 0z"></path></svg></a>genome-to-sqlite</h1> <p><a href="https://pypi.org/project/genome-to-sqlite/" rel="nofollow"><img src="https://camo.githubusercontent.com/a91d14ecfe9aa2d73da4818a7a898033e301380d4c8477d06a17dc20bd871c84/68747470733a2f2f696d672e736869656c64732e696f2f707970692f762f67656e6f6d652d746f2d73716c6974652e737667" alt="PyPI" data-canonical-src="https://img.shields.io/pypi/v/genome-to-sqlite.svg" style="max-width:100%;"></a> <a href="https://circleci.com/gh/dogsheep/genome-to-sqlite" rel="nofollow"><img src="https://camo.githubusercontent.com/5f7f5be2791ff007c49d3d153ef38baa81770a11c0326e5f6b8ffd7ee939d00f/68747470733a2f2f636972636c6563692e636f6d2f67682f646f6773686565702f67656e6f6d652d746f2d73716c6974652e7376673f7374796c653d737667" alt="CircleCI" data-canonical-src="https://circleci.com/gh/dogsheep/genome-to-sqlite.svg?style=svg" style="max-width:100%;"></a> <a href="https://github.com/dogsheep/genome-to-sqlite/blob/master/LICENSE"><img src="https://camo.githubusercontent.com/1698104e976c681143eb0841f9675c6f802bb7aa832afc0c7a4e719b1f3cf955/68747470733a2f2f696d672e736869656c64732e696f2f62616467652f6c6963656e73652d417061636865253230322e302d626c75652e737667" alt="License" data-canonical-src="https://img.shields.io/badge/license-Apache%202.0-blue.svg" style="max-width:100%;"></a></p> <p>Import your genome into a SQLite database.</p> <h2><a id="user-content-how-to-install" class="anchor" aria-hidden="true" href="#user-content-how-to-install"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.775 3.275a.75.75 0 001.06 1.06l1.25-1.25a2 2 0 112.83 2.83l-2.5 2.5a2 2 0 01-2.83 0 .75.75 0 00-1.06 1.06 3.5 3.5 0 004.95 0l2.5-2.5a3.5 3.5 0 00-4.95-4.95l-1.25 1.25zm-4.69 9.64a2 2 0 010-2.83l2.5-2.5a2 2 0 012.83 0 .75.75 0 001.06-1.06 3.5 3.5 0 00-4.95 0l-2.5 2.5a3.5 3.5 0 004.95 4.95l1.25-1.25a.75.75 0 00-1.06-1.06l-1.25 1.25a2 2 0 01-2.83 0z"></path></svg></a>How to install</h2> <div class="snippet-clipboard-content position-relative" data-snippet-clipboard-copy-content="$ pip install genome-to-sqlite "><pre><code>$ pip install genome-to-sqlite </code></pre></div> <h2><a id="user-content-how-to-use" class="anchor" aria-hidden="true" href="#user-content-how-to-use"><svg class="octicon octicon-link" viewBox="0 0 16 16" version="1.1" width="16" height="16" aria-hidden="true"><path fill-rule="evenodd" d="M7.775 3.275a.75.75 0 001.06 1.06l1.25-1.25a2 2 0 112.83 2.83l-2.5 2.5a2 2 0 01-2.83 0 .75.75 0 00-1.06 1.06 3.5 3.5 0 004.95 0l2.5-2.5a3.5 3.5 0 00-4.95-4.95l-1.25 1.25zm-4.69 9.64a2 2 0 010-2.83l2.5-2.5a2 2 0 012.83 0 .75.75 0 001.06-1.06 3.5 3.5 0 00-4.95 0l-2.5 2.5a3.5 3.5 0 004.95 4.95l1.25-1.25a.75.75 0 00-1.06-1.06l-1.25 1.25a2 2 0 01-2.83 0z"></path></svg></a>How to use</h2> <p>First, export your genome. This tool has only been tested against 23andMe so far. You can request an export of your genome from <a href="https://you.23andme.com/tools/data/download/" rel="nofollow">https://you.23andme.com/tools/data/download/</a></p> <p>Now you can convert the resulting <code>export.zip</code> file to SQLite like so:</p> <div class="snippet-clipboard-content position-relative" data-snippet-clipboard-copy-content="$ genome-to-sqlite export.zip genome.db "><pre><code>$ genome-to-sqlite export.zip genome.db </code></pre></div> <p>A progress bar will be displayed. You can disable this using <code>--silent</code>.</p> <div class="snippet-clipboard-content position-relative" data-snippet-clipboard-copy-content="Importing genome [#----------------] 5% 00:01:33 "><pre><code>Importing genome [#----------------] 5% 00:01:33 </code></pre></div> <p>You can explore the resulting data using <a href="https://datasette.readthedocs.io/" rel="nofollow">Datasette</a> like this:</p> <div class="snippet-clipboard-content position-relative" data-snippet-clipboard-copy-content="$ datasette genome.db --config facet_time_limit_ms:1000 "><pre><code>$ datasette genome.db --config facet_time_limit_ms:1000 </code></pre></div> <p>Bumping up the facet time limit is useful in order to enable faceting by chromosome:</p> <p><a href="http://127.0.0.1:8001/genome/genome?_facet=chromosome&_sort=position" rel="nofollow">http://127.0.0.1:8001/genome/genome?_facet=chromosome&_sort=position</a></p> </article></div> |
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