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Link to python API example in api docs
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milot-mirdita committed Jan 4, 2019
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.resource-modal li > ul {
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</style></head><body data-spy="scroll" data-target="#sidebar"><div class="container"><div class="row"><div class="col-md-9" role="main"><div class="page-header"><h1>MMseqs2 Server API documentation <small>version v1</small></h1><p>https://search.mmseqs.com/api</p><p>The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2&#39;s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.</p><p>The ticket object is a basic element of the API. Any job submission returns a ticket. The job status has to be polled based on this ticket. Once a job is in the "COMPLETED" state. Results can be fetched based on the "/result" endpoint.</p></div><div class="panel panel-default"><div class="panel-heading"><h3 id="databases" class="panel-title">/databases</h3></div><div class="panel-body"><div class="top-resource-description"><p>Provides a list of available search databases, including all parameters needed for the frontend.</p></div><div class="panel-group"><div class="panel panel-white resource-modal"><div class="panel-heading"><h4 class="panel-title"><a class="collapsed" data-toggle="collapse" href="#panel_databases"><span class="parent"></span>/databases</a> <span class="methods"><a href="#databases_get"><span class="badge badge_get">get</span></a></span></h4></div><div id="panel_databases" class="panel-collapse collapse"><div class="panel-body"><div class="list-group"><div onclick="window.location.href = '#databases_get'" class="list-group-item"><span class="badge badge_get">get</span><div class="method_description"></div><div class="clearfix"></div></div></div></div></div><div class="modal fade" tabindex="0" id="databases_get"><div class="modal-dialog modal-lg"><div class="modal-content"><div class="modal-header"><button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button><h4 class="modal-title" id="myModalLabel"><span class="badge badge_get">get</span> <span class="parent"></span>/databases</h4></div><div class="modal-body"><div class="resource-description"><p>Provides a list of available search databases, including all parameters needed for the frontend.</p></div><ul class="nav nav-tabs"><li class="active"><a href="#databases_get_response" data-toggle="tab">Response</a></li></ul><div class="tab-content"><div class="tab-pane active" id="databases_get_response"><h2>HTTP status code <a href="http://httpstatus.es/200" target="_blank">200</a></h2><h3>Body</h3><p><strong>Media type</strong>: application/json</p><p><strong>Type</strong>: object</p><strong>Properties</strong><ul><li><strong>databases</strong>: <em>required (array of database)</em><p><strong>Items</strong>: database</p><div class="items"><ul><li><strong>name</strong>: <em>required (string)</em><p>Name of the search database.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>Uniclust30</code></pre></div></li><li><strong>version</strong>: <em>required (string)</em><p>Version of the database.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>2017_10</code></pre></div></li><li><strong>path</strong>: <em>required (string)</em><p>Identifier and path substring.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>uniclust30_2017_07_seed</code></pre></div></li><li><strong>default</strong>: <em>required (boolean)</em><p>If a database is pre-selected by default for a new user.</p></li><li><strong>order</strong>: <em>required (integer)</em><p>In which order the database should be shown in the user interface. 0 is the first.</p></li><li><strong>search</strong>: <em>required (string)</em><p>Extra parameters that are passed to MMseqs2. Useful parameters would be "-s 7" for a high sensitivty search or "--num-iterations 2" for a iterative-profile search.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>-s 7</code></pre></div></li></ul><p><strong>Example</strong>:</p><div class="examples"><pre><code>{
</style></head><body data-spy="scroll" data-target="#sidebar"><div class="container"><div class="row"><div class="col-md-9" role="main"><div class="page-header"><h1>MMseqs2 Server API documentation <small>version v1</small></h1><p>https://search.mmseqs.com/api</p><p>The MMseqs2 desktop and web server app facilitates interactive sequence searches through custom protein sequence and profile databases on personal workstations. By eliminating MMseqs2&#39;s runtime overhead, we reduced response times to a few seconds at sensitivities close to BLAST.</p><p>The ticket object is a basic element of the API. Any job submission returns a ticket. The job status has to be polled based on this ticket. Once a job is in the "COMPLETED" state. Results can be fetched based on the "/result" endpoint.</p><p>A python3 API usage example can be found <a href="https://github.com/soedinglab/MMseqs2-App/blob/master/docs/api_example.py">here</a>.</p></div><div class="panel panel-default"><div class="panel-heading"><h3 id="databases" class="panel-title">/databases</h3></div><div class="panel-body"><div class="top-resource-description"><p>Provides a list of available search databases, including all parameters needed for the frontend.</p></div><div class="panel-group"><div class="panel panel-white resource-modal"><div class="panel-heading"><h4 class="panel-title"><a class="collapsed" data-toggle="collapse" href="#panel_databases"><span class="parent"></span>/databases</a> <span class="methods"><a href="#databases_get"><span class="badge badge_get">get</span></a></span></h4></div><div id="panel_databases" class="panel-collapse collapse"><div class="panel-body"><div class="list-group"><div onclick="window.location.href = '#databases_get'" class="list-group-item"><span class="badge badge_get">get</span><div class="method_description"></div><div class="clearfix"></div></div></div></div></div><div class="modal fade" tabindex="0" id="databases_get"><div class="modal-dialog modal-lg"><div class="modal-content"><div class="modal-header"><button type="button" class="close" data-dismiss="modal" aria-hidden="true">&times;</button><h4 class="modal-title" id="myModalLabel"><span class="badge badge_get">get</span> <span class="parent"></span>/databases</h4></div><div class="modal-body"><div class="resource-description"><p>Provides a list of available search databases, including all parameters needed for the frontend.</p></div><ul class="nav nav-tabs"><li class="active"><a href="#databases_get_response" data-toggle="tab">Response</a></li></ul><div class="tab-content"><div class="tab-pane active" id="databases_get_response"><h2>HTTP status code <a href="http://httpstatus.es/200" target="_blank">200</a></h2><h3>Body</h3><p><strong>Media type</strong>: application/json</p><p><strong>Type</strong>: object</p><strong>Properties</strong><ul><li><strong>databases</strong>: <em>required (array of database)</em><p><strong>Items</strong>: database</p><div class="items"><ul><li><strong>name</strong>: <em>required (string)</em><p>Name of the search database.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>Uniclust30</code></pre></div></li><li><strong>version</strong>: <em>required (string)</em><p>Version of the database.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>2017_10</code></pre></div></li><li><strong>path</strong>: <em>required (string)</em><p>Identifier and path substring.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>uniclust30_2017_07_seed</code></pre></div></li><li><strong>default</strong>: <em>required (boolean)</em><p>If a database is pre-selected by default for a new user.</p></li><li><strong>order</strong>: <em>required (integer)</em><p>In which order the database should be shown in the user interface. 0 is the first.</p></li><li><strong>search</strong>: <em>required (string)</em><p>Extra parameters that are passed to MMseqs2. Useful parameters would be "-s 7" for a high sensitivty search or "--num-iterations 2" for a iterative-profile search.</p><p><strong>Example</strong>:</p><div class="examples"><pre><code>-s 7</code></pre></div></li></ul><p><strong>Example</strong>:</p><div class="examples"><pre><code>{
"name": "Uniclust30",
"version" : "2017_10",
"path" : "uniclust30_2017_10_seed",
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2 changes: 2 additions & 0 deletions docs/api/api.raml
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The ticket object is a basic element of the API. Any job submission returns a ticket. The job status has to be polled based on this ticket.
Once a job is in the "COMPLETED" state. Results can be fetched based on the "/result" endpoint.
A python3 API usage example can be found [here](https://github.com/soedinglab/MMseqs2-App/blob/master/docs/api_example.py).
types:
fasta: string

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