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MicroBIGG-E data at Google Cloud Platform -
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Pathogen Detection - NCBI
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<h1 id="microbigge-data-at-google-cloud-">MicroBIGG-E data at Google Cloud Platform <a href="/pathogens/pathogens_help/#microbigge"><img alt="MicroBIGG-E Documentation TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h1>
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<p><strong>BETA RELEASE</strong> -- <em>This is under active development and while we strive to
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maintain correctness, it is possible results may be unstable, unavailable, or
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incorrect at times. Please contact us by email at pd-help@ncbi.nlm.nih.gov
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before relying on this data for production analyses.</em></p>
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<div class="toc">
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<ul>
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<li><a href="#what-data-is-available-on-the-go">What data is available on the Google Cloud?</a><ul>
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<li><a href="#pathogen-detection-resources-ava">Pathogen Detection Resources available on the Google Cloud</a></li>
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||
<li><a href="#update-frequency">Update Frequency</a></li>
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</ul>
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||
</li>
|
||
<li><a href="#getting-started-with-bigquery">Getting started with BigQuery</a></li>
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||
<li><a href="#linking-to-isolates-browser-data">Linking to Isolates Browser data in BigQuery</a></li>
|
||
<li><a href="#example-searches">Example searches</a><ul>
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||
<li><a href="#find-all-carbapenem-resistance-g">Find all carbapenem resistance genes or point mutations in the database</a></li>
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||
<li><a href="#find-all-carbapenem-resistance-g_1">Find all carbapenem resistance genes in the database</a></li>
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||
<li><a href="#find-all-amrfinderplus-results-f">Find all AMRFinderPlus results from Salmonella genomes for further analysis</a></li>
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||
<li><a href="#find-elements-on-contigs-that-ha">Find elements on contigs that have both blaKPC-2 and blaTEM-1 genes</a></li>
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<li><a href="#find-the-five-most-common-known-">Find the five most common known parC resistance mutations in Pathogen Detection analyzed isolates</a></li>
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<li><a href="#find-the-five-most-common-amr-ge">Find the five most common AMR genes associated with quinolone resistance</a></li>
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||
</ul>
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</li>
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<li><a href="#contig-sequences">Contig sequences</a><ul>
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<li><a href="#example">Example:</a><ul>
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<li><a href="#get-the-contig-sequence-for-a-co">Get the contig sequence for a contig with a point mutation in a specific assembly</a><ul>
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<li><a href="#first-find-the-contig_url-using-">First find the contig_url using BigQuery</a></li>
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||
<li><a href="#copy-the-gzipped-contig-file-usi">Copy the gzipped contig file using the gs utility</a></li>
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||
</ul>
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||
</li>
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||
</ul>
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||
</li>
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||
</ul>
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||
</li>
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||
<li><a href="#protein-sequences">Protein sequences</a><ul>
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||
<li><a href="#examples">Examples:</a><ul>
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||
<li><a href="#get-the-sequence-of-a-single-pro">Get the sequence of a single protein from MicroBIGG-E</a><ul>
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||
<li><a href="#find-the-protein-url-using-bigqu">Find the protein URL using BigQuery</a></li>
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||
<li><a href="#copy-the-gzipped-protein-fasta-f">Copy the gzipped protein FASTA file using the gs utility</a></li>
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||
</ul>
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||
</li>
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||
<li><a href="#download-all-quinolone-resistanc">Download all QUINOLONE resistance genes</a><ul>
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||
<li><a href="#authenticate-the-cli-to-give-it-">Authenticate the CLI to give it permissions on your Google Cloud project</a></li>
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||
<li><a href="#download-a-list-of-urls-using-bq">Download a list of URLs using bq</a></li>
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||
<li><a href="#split-the-list-of-files-into-bat">Split the list of files into batches</a></li>
|
||
<li><a href="#use-a-shell-loop-to-download-the">Use a shell loop to download the protein files</a></li>
|
||
</ul>
|
||
</li>
|
||
</ul>
|
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</li>
|
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</ul>
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</li>
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</ul>
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</div>
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<h2 id="what-data-is-available-on-the-go">What data is available on the Google Cloud? <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
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<p>For a list of all resources see <a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></p>
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||
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<p>The <a href="/pathogens/microbigge">Microbial Browser for Genomic and Genetic Elements</a>
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data is now publicly available in the
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<strong><code>ncbi-pathogen-detect.pdbrowser.microbigge</code></strong> table at Google BigQuery. This
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data includes all the fields available in the browser and can be searched using
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||
<a href="https://cloud.google.com/bigquery/docs/reference/standard-sql/introduction">Google Standard
|
||
SQL</a>
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||
instead of the <a href="/pathogens/pathogens_help/#solr">SOLR Query Language</a>. This
|
||
also permits programmatic access and more complex queries. MicroBIGG-E at
|
||
BigQuery will also allow you to download tables exceeding the 100,000 row limit
|
||
for the <a href="/pathogens/pathogens_help/#microbigge-access-download">MicroBIGG-E web
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||
download</a>. NCBI is
|
||
piloting this in BigQuery to help users leverage the benefits of elastic
|
||
scaling and parallel execution of queries. BigQuery has a large collection of
|
||
client libraries that can be used within your workflow. You can also interact
|
||
with it on a web browser as described below. </p>
|
||
|
||
<p>We also are storing the contig sequences and protein sequences for MicroBIGG-E
|
||
hits in Google Storage buckets. See <a href="#contig-sequences">Contig sequences</a> and
|
||
<a href="#protein-sequences">Protein sequences</a> below for more information.</p>
|
||
|
||
<h3 id="pathogen-detection-resources-ava">Pathogen Detection Resources available on the Google Cloud</h3>
|
||
|
||
<ul>
|
||
<li><a href="/pathogens/docs/gcp/">Pathogen Detection Resources at Google Cloud Platform</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp/#getting-started-with-bigquery">Getting started with BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp/">MicroBIGG-E table in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp/#contig-sequences">MicroBIGG-E contig sequences in Google Storage buckets</a></li>
|
||
<li><a href="/pathogens/docs/microbigge_gcp/#protein-sequences">MicroBIGG-E protein sequences in Google Storage buckets</a></li>
|
||
<li><a href="/pathogens/docs/ast_gcp/">AST Browser in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/isolates_gcp/">Isolates Browser table in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/isolates_gcp/#isolate_exceptions">Isolate Exceptions table in BigQuery</a></li>
|
||
<li><a href="/pathogens/docs/bioproject_hierarchy_gcp/">BioProject Hierarchy in BigQuery</a>
|
||
<!-- asdf_ -->
|
||
</li>
|
||
</ul>
|
||
|
||
<h3 id="update-frequency">Update Frequency <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<p>The microbigge table at Google Cloud BigQuery is updated daily. For this reason the contents may
|
||
not agree exactly with those shown in the <a href="/pathogens/microbigge">MicroBIGG-E web
|
||
browser</a>. If you see unexpected discrepancies please let us know by emailing us at pd-help@ncbi.nlm.nih.gov.</p>
|
||
|
||
<h2 id="getting-started-with-bigquery"><a href="/pathogens/docs/getting_started_bigquery">Getting started with BigQuery</a></h2>
|
||
|
||
<p>Our <a href="/pathogens/docs/getting_started_bigquery">Getting started with BigQuery</a> page has instructions on how to run queries with BigQuery.</p>
|
||
|
||
<h2 id="linking-to-isolates-browser-data">Linking to Isolates Browser data in BigQuery</h2>
|
||
|
||
<p>NCBI Pathogen Detection also maintains <a href="/pathogens/pathogens_help/#isolates-browser">Isolates Browser</a> data in the BigQuery table <code>ncbi-pathogen-detect.pdbrowser.isolates</code>. There are several fields in common between the two tables, but we generally recommend joining on the <code>target_acc</code> field. See <a href="/pathogens/docs/isolates_gcp">Isolates Browser Data at Google Cloud Platform</a> for examples of joining the two tables.</p>
|
||
|
||
<h2 id="example-searches">Example searches <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
|
||
|
||
<h3 id="find-all-carbapenem-resistance-g">Find all carbapenem resistance genes or point mutations in the database <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT *
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
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||
WHERE subclass like '%CARBAPENEM%'
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||
ORDER BY element_symbol, closest_reference_acc, target_acc, protein_acc
|
||
</code></pre>
|
||
|
||
<h3 id="find-all-carbapenem-resistance-g_1">Find all carbapenem resistance genes in the database <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT *
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE subclass like '%CARBAPENEM%'
|
||
AND subtype = 'AMR'
|
||
ORDER BY element_symbol, closest_reference_acc, target_acc, protein_acc
|
||
</code></pre>
|
||
|
||
<h3 id="find-all-amrfinderplus-results-f">Find all AMRFinderPlus results from Salmonella genomes for further analysis <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT *
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE taxgroup_name = 'Salmonella enterica'
|
||
</code></pre>
|
||
|
||
<h3 id="find-elements-on-contigs-that-ha">Find elements on contigs that have both blaKPC-2 and blaTEM-1 genes <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT
|
||
mb.contig_acc,
|
||
mb.element_symbol
|
||
FROM
|
||
`ncbi-pathogen-detect.pdbrowser.microbigge` mb
|
||
JOIN ( SELECT DISTINCT
|
||
mb1.contig_acc
|
||
FROM
|
||
`ncbi-pathogen-detect.pdbrowser.microbigge` mb1
|
||
JOIN `ncbi-pathogen-detect.pdbrowser.microbigge` mb2
|
||
ON mb1.element_symbol = 'blaTEM-1'
|
||
AND mb1.contig_acc = mb2.contig_acc
|
||
AND mb2.element_symbol = 'blaKPC-2') contigs
|
||
ON contigs.contig_acc = mb.contig_acc
|
||
ORDER BY
|
||
mb.contig_acc,
|
||
mb.start_on_contig
|
||
</code></pre>
|
||
|
||
<h3 id="find-the-five-most-common-known-">Find the five most common known parC resistance mutations in Pathogen Detection analyzed isolates <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT element_symbol, count(*) num_found
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE element_symbol like 'parC_%'
|
||
GROUP BY element_symbol
|
||
ORDER BY num_found DESC
|
||
LIMIT 5
|
||
</code></pre>
|
||
|
||
<h3 id="find-the-five-most-common-amr-ge">Find the five most common AMR genes associated with quinolone resistance <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<pre><code>SELECT element_symbol, subclass, count(*) num_found
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE subclass like '%QUINOLONE%'
|
||
AND subtype = 'AMR'
|
||
GROUP BY element_symbol, subclass
|
||
ORDER BY num_found DESC
|
||
LIMIT 5
|
||
</code></pre>
|
||
|
||
<h2 id="contig-sequences">Contig sequences<a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
|
||
|
||
<p>Contig sequences in gzipped FASTA format are stored and accessible in the Google storage bucket <code>ncbi-pathogen-assemblies</code> and the paths to those contigs are listed in the <code>ncbi-pathogen-detect.pdbrowser.microbigge</code> field <code>contig_url</code>.</p>
|
||
|
||
<p>These can be accessed using the <code>gsutil</code> command-line program included with the <a href="https://cloud.google.com/sdk/docs">Google Cloud CLI</a> (<a href="https://cloud.google.com/storage/docs/gsutil_install">Installation instructions</a>). Or through the GCP BigQuery web interface. See <a href="/pathogens/docs/getting_started_bigquery/">Getting started with BigQuery</a> for more information on how to use BigQuery.</p>
|
||
|
||
<h3 id="example">Example: <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<h4 id="get-the-contig-sequence-for-a-co">Get the contig sequence for a contig with a point mutation in a specific assembly <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h4>
|
||
|
||
<h5 id="first-find-the-contig_url-using-">First find the contig_url using BigQuery <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<pre><code>SELECT contig_url
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE element_symbol = 'ompK36_D135DGD'
|
||
AND biosample_acc = 'SAMN01057611';
|
||
</code></pre>
|
||
|
||
<p>The results should be:</p>
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>contig_url</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>gs://ncbi-pathogen-assemblies/Klebsiella/9/640/NZ_CP008827.1.fna.gz</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
<h5 id="copy-the-gzipped-contig-file-usi">Copy the gzipped contig file using the <code>gs</code> utility <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<p>Enter the following at a unix shell command-line to copy the gzipped contig FASTA file to your computer. See the <a href="https://cloud.google.com/storage/docs/gsutil">Google docs</a> for more information on the gsutil program.</p>
|
||
|
||
<pre><code>gsutil cp gs://ncbi-pathogen-assemblies/Klebsiella/9/640/NZ_CP008827.1.fna.gz .
|
||
</code></pre>
|
||
|
||
<h2 id="protein-sequences">Protein sequences<a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h2>
|
||
|
||
<p>Protein sequences in gzipped FASTA format are stored and accessible in the Google Storage bucket <code>ncbi-pathogen-assemblies</code> and the paths to those files are listed in the <code>ncbi-pathogen-detect.pdbrowser.microbigge</code> field <code>protein_url</code>.</p>
|
||
|
||
<p>These can be accessed using the <code>gsutil</code> command-line program included with the <a href="https://cloud.google.com/sdk/docs">Google Cloud CLI</a> (<a href="https://cloud.google.com/storage/docs/gsutil_install">Installation instructions</a>). Or through the GCP BigQuery web interface. See <a href="/pathogens/docs/getting_started_bigquery/">Getting started with BigQuery</a> for more information on how to use BigQuery.</p>
|
||
|
||
<h3 id="examples">Examples: <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h3>
|
||
|
||
<h4 id="get-the-sequence-of-a-single-pro">Get the sequence of a single protein from MicroBIGG-E <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h4>
|
||
|
||
<h5 id="find-the-protein-url-using-bigqu">Find the protein URL using BigQuery <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<pre><code>SELECT protein_url
|
||
FROM `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
WHERE element_symbol = 'ompK36_D135DGD'
|
||
AND biosample_acc = 'SAMN01057611';
|
||
</code></pre>
|
||
|
||
<p>The results should be:</p>
|
||
|
||
<table>
|
||
<thead>
|
||
<tr>
|
||
<th>protein_url</th>
|
||
</tr>
|
||
</thead>
|
||
<tbody>
|
||
<tr>
|
||
<td>gs://ncbi-pathogen-proteins/WP_/004/151/WP_004151112.1.faa.gz</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
<h5 id="copy-the-gzipped-protein-fasta-f">Copy the gzipped protein FASTA file using the <code>gs</code> utility <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<p>Enter the following at a unix shell command-line to copy the gzipped contig FASTA file to your computer. See the <a href="https://cloud.google.com/storage/docs/gsutil">Google docs</a> for more information on the gsutil program.</p>
|
||
|
||
<pre><code>gsutil cp gs://ncbi-pathogen-proteins/WP_/004/151/WP_004151112.1.faa.gz .
|
||
</code></pre>
|
||
|
||
<h4 id="download-all-quinolone-resistanc">Download all QUINOLONE resistance genes <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h4>
|
||
|
||
<p>This example uses a Linux or MacOS command-line, the <a href="https://cloud.google.com/sdk/gcloud">Google cloud CLI</a>, and the bash shell. See <a href="https://cloud.google.com/sdk/docs/install-sdk">Install the Google Cloud CLI</a> documentation from Google for instructions of how to install the CLI. </p>
|
||
|
||
<h5 id="authenticate-the-cli-to-give-it-">Authenticate the CLI to give it permissions on your Google Cloud project <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<p>See <a href="https://cloud.google.com/sdk/docs/initializing">Initializing the gcloud CLI</a> for more information.</p>
|
||
|
||
<pre><code>gcloud auth login
|
||
</code></pre>
|
||
|
||
<p>Follow instructions to authenticate to google cloud</p>
|
||
|
||
<h5 id="download-a-list-of-urls-using-bq">Download a list of URLs using <code>bq</code> <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<pre><code>bq query --use_legacy_sql=false --format=csv --max_rows 300000 '
|
||
select distinct protein_url
|
||
from `ncbi-pathogen-detect.pdbrowser.microbigge`
|
||
where class = "%QUINOLONE%"
|
||
' > all_quinolone_urls.csv
|
||
</code></pre>
|
||
|
||
<h5 id="split-the-list-of-files-into-bat">Split the list of files into batches <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<p>We do this because directories tend to have performance issues when there are too many files in one directory. Depending on your operating system and configuration you could change the size of the batches.</p>
|
||
|
||
<pre><code>split -d -l 5000 all_quinolone_urls.csv batch.
|
||
</code></pre>
|
||
|
||
<h5 id="use-a-shell-loop-to-download-the">Use a shell loop to download the protein files <a href="#TOC"><img alt="MicroBIGG-E at Google Cloud Platform TOC" src="/core/assets/pathogens/images/toc_icon.png"/></a> <a href="/pathogens/pathogens_help/"><img alt="Main documentation page" src="/core/assets/pathogens/images/arrowup_blue.gif"/></a></h5>
|
||
|
||
<pre><code>for file in batch.*
|
||
do
|
||
mkdir $file.asm
|
||
cat $file | gcloud alpha storage cp --read-paths-from-stdin $file.asm/
|
||
done
|
||
</code></pre>
|
||
|
||
</div>
|
||
|
||
|
||
|
||
</section>
|
||
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