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<!DOCTYPE html>
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<head>
<meta charset="utf-8">
<meta name="generator" content="pandoc">
<meta name="author" content="Colin A. Gross">
<meta name="dcterms.date" content="2021-09-13">
<title>BRAVO 2021</title>
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</head>
<body>
<div class="reveal">
<div class="slides">
<section id="title-slide">
<h1 class="title">BRAVO 2021</h1>
<p class="author">Colin A. Gross</p>
<p class="date">2021-09-13</p>
</section>
<section>
<section id="bravo-for-your-vcfs" class="title-slide slide level1">
<h1>BRAVO for your VCFs</h1>
<p>“Spin up and instance with your VCFs!”</p>
</section>
<section id="spinup-steps" class="slide level2">
<h2>Spinup Steps</h2>
<ol type="1">
<li>Prepare Data: (<a href="https://github.com/statgen/bravo_data_prep">Bravo Data Prep</a>) ✓</li>
<li>Deploy Data: (<a href="https://github.com/statgen/bravo_api">Bravo API</a>) ✓</li>
<li>Deploy API: (<a href="https://github.com/statgen/bravo_api">Bravo API</a>) ✓</li>
<li>Deply UI: (<a href="https://github.com/grosscol/vue_mpa_prototype">Bravo Vue UI</a>) ◎</li>
</ol>
</section>
<section id="inputs" class="slide level2">
<h2>Inputs</h2>
<ul>
<li>VCFs</li>
<li>Crams</li>
</ul>
</section>
<section id="software-dependencies" class="slide level2">
<h2>Software Dependencies</h2>
<ul>
<li>Nextflow, python, tabix, samtools, htslib, VEP, BamUtil, Loftee</li>
<li>Flask, pymongo, mongodb</li>
<li>Npm, vue-cli</li>
</ul>
</section>
<section id="data-dependencies" class="slide level2">
<h2>Data Dependencies</h2>
<p>HUGO names, Ensembl Id mapping, OMIM mapping, Gencode gene list, loftee ancestor.fa, loftee conservation files, reference sequence</p>
</section></section>
<section>
<section id="current-state-data-prep" class="title-slide slide level1">
<h1>Current State: Data Prep</h1>
<p>Consolidated and coherent</p>
</section>
<section id="consolidate-data-processing-scripts" class="slide level2">
<h2>✓ Consolidate data processing scripts</h2>
<pre><code>workflows/
├── coverage
│ ├── Coverage.nf
│ └── nextflow.config
├── prepare_vcf
│ ├── PrepareVCF.nf
│ └── nextflow.config
└── sequences
├── Sequences.nf
└── nextflow.config</code></pre>
</section>
<section id="document-data-processing-config" class="slide level2">
<h2>✓ Document data processing config</h2>
<div class="sourceCode" id="cb2"><pre class="sourceCode groovy"><code class="sourceCode groovy"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a> <span class="co">// Use wildcard like chr11.*.bcf for list of bcf files.</span></span>
<span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a> chromosome <span class="op">=</span> <span class="st">"chr11"</span></span>
<span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a> <span class="co">// Required input data</span></span>
<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a> vcfs <span class="op">=</span> <span class="st">"data/chr11.subset.bcf"</span></span>
<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a> <span class="co">// Use *.tsv.gz for list of cadd files.</span></span>
<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a> cadd_tsvs <span class="op">=</span> <span class="st">"data/chr11.sites.cadd.tsv.gz"</span></span>
<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a> <span class="co">// Optional input data</span></span>
<span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a> <span class="co">// Use NO_FILE to indicate the optional samples list is not being used.</span></span>
<span id="cb2-11"><a href="#cb2-11" aria-hidden="true" tabindex="-1"></a> samples <span class="op">=</span> <span class="st">"NO_FILE"</span></span>
<span id="cb2-12"><a href="#cb2-12" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-13"><a href="#cb2-13" aria-hidden="true" tabindex="-1"></a> <span class="co">// Executeable paths.</span></span>
<span id="cb2-14"><a href="#cb2-14" aria-hidden="true" tabindex="-1"></a> <span class="co">// Use name of exec if in PATH or is symlinked in bin/ of this pipeline</span></span>
<span id="cb2-15"><a href="#cb2-15" aria-hidden="true" tabindex="-1"></a> vep <span class="op">=</span> <span class="st">"vep"</span></span>
<span id="cb2-16"><a href="#cb2-16" aria-hidden="true" tabindex="-1"></a> counts_exec <span class="op">=</span> <span class="st">"ComputeAlleleCountsAndHistograms"</span></span>
<span id="cb2-17"><a href="#cb2-17" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb2-18"><a href="#cb2-18" aria-hidden="true" tabindex="-1"></a> <span class="co">// Scripts use full path or path to symlink in local bin/</span></span>
<span id="cb2-19"><a href="#cb2-19" aria-hidden="true" tabindex="-1"></a> add_cadd_script <span class="op">=</span> <span class="st">"bin/add_cadd_scores.py"</span></span></code></pre></div>
</section>
<section id="document-software-dependencies" class="slide level2">
<h2>✓ Document software dependencies</h2>
<pre><code>## BamUtil
Clone and install from [bamUtil repo](https://github.com/statgen/bamUtil)
## VEP
Installation [instructions](https://useast.ensembl.org/info/docs/tools/vep/script/vep_download.html) on ensembl.org.
## Loftee
Master branch of [LoF plugin](https://github.com/konradjk/loftee) doesn't work for GRCh38
per this [issue](https://github.com/konradjk/loftee/issues/73#issuecomment-733109901)
```
git clone --depth 1 --branch grch38 --single-branch git@github.com:konradjk/loftee.git
```</code></pre>
</section>
<section id="document-data-dependencies" class="slide level2">
<h2>✓ Document data dependencies</h2>
<pre><code>#### Genenames: HUGO Gene Nomenclature Commitee (HGNC)
Can be obtained from [genenames custom downloads](https://www.genenames.org/download/custom/)
The genenames set from all the chromosomes with the above columns can be obtained using curl.
```
curl 'https://www.genenames.org/cgi-bin/...
```</code></pre>
<p>and idiosyncracies</p>
<pre><code>Headers need to be rewritten to match expected column names and the results gzipped
```
echo -e "symbol\tname\talias_symbol\tprev_symbol\tensembl_gene_id" > hgcn_genenames.txt
tail -n +2 hgcn_custom_result.txt >> hgcn_genenames.txt
gzip hgcn_genenames.txt
```</code></pre>
</section>
<section id="update-dependencies" class="slide level2">
<h2>✓ Update dependencies</h2>
<ul>
<li>hstlib, samtools, bamtools, tabix, vcftools</li>
<li>python packages & scripts</li>
<li>Nextflow 1.x -> 2.0</li>
</ul>
</section></section>
<section>
<section id="current-state-api" class="title-slide slide level1">
<h1>Current State: API</h1>
<p>Up to date & operational</p>
</section>
<section id="dependency-updates" class="slide level2">
<h2>✓ Dependency Updates</h2>
<ul>
<li>marshmallow</li>
<li>pymongo</li>
<li>pysam</li>
</ul>
</section>
<section id="refactor-framework-code" class="slide level2">
<h2>✓ Refactor Framework Code</h2>
<p>Explicit calls to web arg parsing</p>
<div class="sourceCode" id="cb6"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="at">@bp.route</span>(<span class="st">'/coverage'</span>, methods <span class="op">=</span> [<span class="st">'GET'</span>])</span>
<span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="kw">def</span> get_coverage():</span>
<span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a> arguments <span class="op">=</span> {</span>
<span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a> <span class="st">'chrom'</span>: fields.Str(required <span class="op">=</span> <span class="va">True</span>, validate ... ),</span>
<span id="cb6-5"><a href="#cb6-5" aria-hidden="true" tabindex="-1"></a> <span class="st">'start'</span>: fields.Int(required <span class="op">=</span> <span class="va">True</span>, validate ...), }</span>
<span id="cb6-6"><a href="#cb6-6" aria-hidden="true" tabindex="-1"></a> args <span class="op">=</span> parser.parse(arguments,</span>
<span id="cb6-7"><a href="#cb6-7" aria-hidden="true" tabindex="-1"></a> validate <span class="op">=</span> partial(validate_coverage_http_request_args ...```</span></code></pre></div>
<p>Framework decorator</p>
<div class="sourceCode" id="cb7"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>cov_argmap <span class="op">=</span> {</span>
<span id="cb7-2"><a href="#cb7-2" aria-hidden="true" tabindex="-1"></a> <span class="st">'chrom'</span>: fields.Str(required <span class="op">=</span> <span class="va">True</span>, validate ...),</span>
<span id="cb7-3"><a href="#cb7-3" aria-hidden="true" tabindex="-1"></a> <span class="st">'start'</span>: fields.Int(required <span class="op">=</span> <span class="va">True</span>, validate ...), }</span>
<span id="cb7-4"><a href="#cb7-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb7-5"><a href="#cb7-5" aria-hidden="true" tabindex="-1"></a><span class="at">@bp.route</span>(<span class="st">'/coverage'</span>, methods<span class="op">=</span>[<span class="st">'GET'</span>])</span>
<span id="cb7-6"><a href="#cb7-6" aria-hidden="true" tabindex="-1"></a><span class="at">@use_args</span>(cov_argmap, location<span class="op">=</span><span class="st">'query'</span>, validate<span class="op">=</span>validate_paging_args)</span>
<span id="cb7-7"><a href="#cb7-7" aria-hidden="true" tabindex="-1"></a><span class="kw">def</span> get_coverage(args):</span></code></pre></div>
</section>
<section id="package" class="slide level2">
<h2>✓ Package</h2>
<p>Allows for editable install to avoid local ENV complications.</p>
<div class="sourceCode" id="cb8"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="ex">python</span> <span class="at">-m</span> pip install <span class="at">-e</span> .[dev,test]</span></code></pre></div>
<p>Actual test tooling to separate integration & unit tests.</p>
<div class="sourceCode" id="cb9"><pre class="sourceCode ini"><code class="sourceCode ini"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="kw">[pytest]</span></span>
<span id="cb9-2"><a href="#cb9-2" aria-hidden="true" tabindex="-1"></a><span class="dt">testpaths </span><span class="ot">=</span></span>
<span id="cb9-3"><a href="#cb9-3" aria-hidden="true" tabindex="-1"></a><span class="dt"> tests</span></span>
<span id="cb9-4"><a href="#cb9-4" aria-hidden="true" tabindex="-1"></a><span class="dt">mongodb_fixture_dir </span><span class="ot">=</span><span class="st"> </span></span>
<span id="cb9-5"><a href="#cb9-5" aria-hidden="true" tabindex="-1"></a><span class="dt"> tests/mongo_fixtures</span></span>
<span id="cb9-6"><a href="#cb9-6" aria-hidden="true" tabindex="-1"></a><span class="dt">markers </span><span class="ot">=</span></span>
<span id="cb9-7"><a href="#cb9-7" aria-hidden="true" tabindex="-1"></a><span class="dt"> integration: using actual data or actual mongodb. (run using --integration)</span></span>
<span id="cb9-8"><a href="#cb9-8" aria-hidden="true" tabindex="-1"></a><span class="dt"> default: applied by top level conftest.py to otherwise unmarked tests.</span></span></code></pre></div>
</section>
<section id="define-io-data" class="slide level2">
<h2>✓ Define I/O Data</h2>
<p>Mongo fixtures <code>tests/fixtures/genes.json</code></p>
<div class="sourceCode" id="cb10"><pre class="sourceCode json"><code class="sourceCode json"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a> <span class="er">"chrom":</span> <span class="er">"5",</span></span>
<span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a> <span class="er">"start":</span> <span class="er">10736171,</span></span>
<span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a> <span class="er">"xstart":</span> <span class="fu">{</span> <span class="dt">"$numberLong"</span><span class="fu">:</span> <span class="st">"5010736171"</span> <span class="fu">}</span><span class="er">,</span></span></code></pre></div>
<p>Endpoint expectations defined tests.</p>
<div class="sourceCode" id="cb11"><pre class="sourceCode python"><code class="sourceCode python"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a>GENE_RESULT <span class="op">=</span> [</span>
<span id="cb11-2"><a href="#cb11-2" aria-hidden="true" tabindex="-1"></a> {<span class="st">'chrom'</span>: <span class="st">'11'</span>, <span class="st">'full_gene_name'</span>: <span class="st">'hemoglobin subunit beta pseudogene 1'</span>,</span>
<span id="cb11-3"><a href="#cb11-3" aria-hidden="true" tabindex="-1"></a> <span class="st">'gene_id'</span>: <span class="st">'ENSG00000229988'</span>, <span class="st">'gene_name'</span>: <span class="st">'HBBP1'</span>)</span></code></pre></div>
</section></section>
<section>
<section id="current-state-ui" class="title-slide slide level1">
<h1>Current State: UI</h1>
<p>Moving to Vue</p>
</section>
<section id="move-server-side-functions-to-api" class="slide level2">
<h2>✓ Move Server Side Functions to API</h2>
</section>
<section id="simplify-build-deploy" class="slide level2">
<h2>✓ Simplify Build & Deploy</h2>
<p>Previously:</p>
<ol type="1">
<li>build each vue component</li>
<li>copy all dist/ directories to flask assets</li>
<li>serve flask app</li>
</ol>
<p>Currently:</p>
<div class="sourceCode" id="cb12"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="ex">npm</span> run serve</span></code></pre></div>
</section>
<section id="consolidate-components" class="slide level2">
<h2>◎ Consolidate Components</h2>
<p>TODO: Migrate all .vue components under single application.</p>
<div class="sourceCode" id="cb13"><pre class="sourceCode sh"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="ex">workspace/ui_bravo2/web_components/</span></span>
<span id="cb13-2"><a href="#cb13-2" aria-hidden="true" tabindex="-1"></a><span class="ex">├──</span> bravo-model</span>
<span id="cb13-3"><a href="#cb13-3" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> ├── package.json</span>
<span id="cb13-4"><a href="#cb13-4" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> └── src</span>
<span id="cb13-5"><a href="#cb13-5" aria-hidden="true" tabindex="-1"></a><span class="ex">├──</span> bravo-region</span>
<span id="cb13-6"><a href="#cb13-6" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> ├── package.json</span>
<span id="cb13-7"><a href="#cb13-7" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> └── src</span>
<span id="cb13-8"><a href="#cb13-8" aria-hidden="true" tabindex="-1"></a><span class="ex">├──</span> bravo-search</span>
<span id="cb13-9"><a href="#cb13-9" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> ├── package.json</span>
<span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a><span class="ex">│ </span> └── src</span>
<span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a><span class="ex">└──</span> bravo-variant</span>
<span id="cb13-12"><a href="#cb13-12" aria-hidden="true" tabindex="-1"></a> <span class="ex">├──</span> package.json</span>
<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a> <span class="ex">└──</span> src</span></code></pre></div>
</section>
<section id="test-components" class="slide level2">
<h2>◎ Test Components</h2>
<p>TODO: Verify expected appearance & behavior</p>
<div class="sourceCode" id="cb14"><pre class="sourceCode js"><code class="sourceCode javascript"><span id="cb14-1"><a href="#cb14-1" aria-hidden="true" tabindex="-1"></a><span class="fu">it</span>(<span class="st">"Horizontal rule gets centered"</span><span class="op">,</span> () <span class="kw">=></span> {</span>
<span id="cb14-2"><a href="#cb14-2" aria-hidden="true" tabindex="-1"></a> <span class="fu">expect</span>(cmp<span class="op">.</span><span class="fu">find</span>(Message)<span class="op">.</span><span class="fu">attributes</span>()<span class="op">.</span><span class="at">style</span>)<span class="op">.</span><span class="fu">toBe</span>(<span class="st">"padding-top: 10px;"</span>)<span class="op">;</span></span>
<span id="cb14-3"><a href="#cb14-3" aria-hidden="true" tabindex="-1"></a>})<span class="op">;</span></span>
<span id="cb14-4"><a href="#cb14-4" aria-hidden="true" tabindex="-1"></a></span>
<span id="cb14-5"><a href="#cb14-5" aria-hidden="true" tabindex="-1"></a><span class="fu">it</span>(<span class="st">'centers horizontal rule'</span><span class="op">,</span> () <span class="kw">=></span> {</span>
<span id="cb14-6"><a href="#cb14-6" aria-hidden="true" tabindex="-1"></a> <span class="kw">const</span> wrapper <span class="op">=</span> <span class="fu">shallowMount</span>(SearchBox<span class="op">,</span> { <span class="dt">props</span><span class="op">:</span> { <span class="dt">autofocus</span><span class="op">:</span> <span class="kw">true</span> } })</span>
<span id="cb14-7"><a href="#cb14-7" aria-hidden="true" tabindex="-1"></a> <span class="kw">const</span> hrStyle <span class="op">=</span> wrapper<span class="op">.</span><span class="fu">find</span>(<span class="st">'hr'</span>)<span class="op">.</span><span class="fu">attributes</span>()<span class="op">.</span><span class="at">style</span></span>
<span id="cb14-8"><a href="#cb14-8" aria-hidden="true" tabindex="-1"></a> <span class="fu">expect</span>(hrStyle)<span class="op">.</span><span class="at">to</span><span class="op">.</span><span class="fu">include</span>(<span class="st">'margin-right: auto'</span>)</span>
<span id="cb14-9"><a href="#cb14-9" aria-hidden="true" tabindex="-1"></a> <span class="fu">expect</span>(hrStyle)<span class="op">.</span><span class="at">to</span><span class="op">.</span><span class="fu">include</span>(<span class="st">'margin-left: auto'</span>)</span>
<span id="cb14-10"><a href="#cb14-10" aria-hidden="true" tabindex="-1"></a>})</span></code></pre></div>
</section></section>
<section>
<section id="next-work" class="title-slide slide level1">
<h1>Next work</h1>
</section>
<section id="short-term" class="slide level2">
<h2>Short Term</h2>
<ul>
<li>Finish UI Migration</li>
<li>Update deployment playbook</li>
<li>Test Data Prep Pipeline with freeze10 data.</li>
<li>Test Data Prep Pipeline with public data.</li>
<li>Advertise</li>
</ul>
</section>
<section id="mid-term" class="slide level2">
<h2>Mid Term</h2>
<ul>
<li>Reduce Data Prep requirements</li>
<li>Better handle <em>missing</em> info</li>
<li>Flask app deployment plan for SPH infrastructure</li>
</ul>
</section>
<section id="long-term" class="slide level2">
<h2>Long Term</h2>
<ul>
<li>Continuous Integration via GH Actions</li>
<li>External deployments & collaboration</li>
</ul>
</section></section>
<section id="end" class="title-slide slide level1">
<h1>End</h1>
</section>
</div>
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