cb718a9f9f9d2c9d43a92a618da91be0de85ed3d hiram Mon Jul 21 16:32:16 2025 -0700 document the findGenome endpoint and reveal the /list/genarkGenomes endpoing function refs #35468 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index b712d0a1358..95bda4c5860 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -96,30 +96,31 @@ <h2>What is the access URL?</h2> <p> This access URL: <b>https://api.genome.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> wget -O- 'https://api.genome.ucsc.edu/list/publicHubs' </pre> </p> <!-- ========== What type of data can be accessed? ===================== --> <a id="Return"></a> <h2>What type of data can be accessed?</h2> <p> The following data sets can be accessed at this time: <ul> +<li>Find a genome in the UCSC browser with a search string</li> <li>List of available public hubs</li> <li>List of available UCSC Genome Browser genome assemblies</li> <li>List of files available for download for UCSC Browser genome assemblies</li> <li>List of genomes from a specified assembly or track hub</li> <li>List of available data tracks from a specified hub or UCSC Genome Browser genome assembly (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li> <li>List of chromosomes contained in an assembly hub or UCSC Genome Browser genome assembly</li> <li>List of chromosomes contained in a specific track of an assembly or track hub, or UCSC Genome Browser genome assembly</li> <li>Return DNA sequence from an assembly hub 2bit file, or UCSC Genome Browser assembly</li> <li>Return track data from a specified assembly or track hub, or UCSC Genome Browser assembly</li> <li>Return search matches to words in track data, track names, track descriptions, public hub track names, and public hub descriptions within a UCSC Genome Browser genome assembly</li> </ul> @@ -127,100 +128,107 @@ <a href="/FAQ/FAQblat.html#blat14">BLAT FAQ</a> for more info. </p> <!-- ========== Endpoint functions ======================= --> <a id="Endpoint"></a> <h2>Endpoint functions to return data</h2> <p> The URL <b>https://api.genome.ucsc.edu/</b> is used to access the endpoint functions. For example: <pre> curl -L 'https://api.genome.ucsc.edu/list/ucscGenomes' </pre> </p> <p> <ul> +<li><b>/findGenome</b> - search for a genome in the UCSC browser</li> <li><b>/list/publicHubs</b> - list public hubs</li> <li><b>/list/ucscGenomes</b> - list UCSC Genome Browser database genomes from database host</li> -<!-- not yet <li><b>/list/genarkGenomes</b> - list UCSC Genome Browser database genomes from assembly hub host</li> ---> <li><b>/list/hubGenomes</b> - list genomes from specified hub</li> <li><b>/list/files</b> - list download files available for specified genome</li> <li><b>/list/tracks</b> - list data tracks available in specified hub or database genome (see also: <a href='trackDb/trackDbHub.html' target=_blank>track definition help</a>)</li> <li><b>/list/chromosomes</b> - list chromosomes from a data track in specified hub or database <li><b>/list/schema</b> - list the schema for a data track in specified hub or database genome</li> <li><b>/getData/sequence</b> - return sequence from specified hub or database genome</li> <li><b>/getData/track</b> - return data from specified track in hub or database genome</li> <li><b>/search</b> - return search matches within a UCSC Genome Browser genome assembly</li> </ul> </p> <!-- ========== Parameters to endpoint functions ======================= --> <a id="Parameters"></a> <h2>Parameters to endpoint functions</h2> <p> <ul> +<li>maxItemsOutput=1000000 - limit number of items to output, default: 1,000,000, maximum limit: +1,000,000 (use <em>-1</em> to get maximum output)</li> <li>hubUrl=<url> - specify track hub or assembly hub URL</li> <li>genome=<name> - specify genome assembly in UCSC Genome Browser or track/assembly hub. Use with with /list/genarkGenomes to test for existence.</li> <li>track=<trackName> - specify data track in track/assembly hub or UCSC database genome assembly</li> <li>chrom=<chrN> - specify chromosome name for sequence or track data</li> <li>start=<123> - specify start coordinate (0 relative) for data from track or sequence retrieval (start and end required together). See also: <a href='https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems</a></li> <li>end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together). See also: <a href='https://genome-blog.gi.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems</a></li> -<li>revComp=1 - on <em>/getData/sequence</em> function, return reverse complement of sequence data</li> -<li>maxItemsOutput=1000 - limit number of items to output, default: 1,000, maximum limit: -1,000,000 (use <em>-1</em> to get maximum output)</li> +<li>q=<search word(s)> - used with <em>/findGenome</em>, a search string</li> +<li>browser=<mustExist|mayExist|notExist> - used with <em>/findGenome</em>, <em>mustExist</em> result only for assemblies in the UCSC browser, <em>mayExist</em> may exist in the UCSC browser, or may not, <em>notExist</em> not yet available in the browser. default is <em>mustExist</em> </li> +<li>statsOnly=1 - on <em>/findGenome</em> function, only show statistics about search result</li> +<li>year=<2025> - on <em>/findGenome</em> function, only show search result for given year, default is any year</li> +<li>category=<reference|representative> - on <em>/findGenome</em> function, show search result only for given NCBI category of assembly</li> +<li>status=<reference|representative> - on <em>/findGenome</em> function, show search result only for given NCBI status of assembly</li> +<li>level=<complete|chromosome|scaffold|contig> - on <em>/findGenome</em> function, show search result only for given NCBI level of assembly</li> <li>trackLeavesOnly=1 - on <em>/list/tracks</em> function, only show tracks, do not show composite container information</li> +<li>revComp=1 - on <em>/getData/sequence</em> function, return reverse complement of sequence data</li> <li>jsonOutputArrays=1 - on <em>/getData/track</em> function, JSON format is array type for each item of data, instead of the default object type</li> <li>format=text - on <em>/list/files</em> function, return plain text listing of download files instead of JSON format output (which includes more meta-data information). Text output contains less meta-data in comment lines prefixed by the '#' hash character.</li> <li>search=<term>&genome=<name> - on <em>/search</em> function, specify term to be search within a UCSC Genome Browser genome assembly</li> <li>categories=helpDocs - on <em>/search?search=<term>&genome=<name></em> function, restrict the search within the UCSC Genome Browser help documentation</li> <li>categories=publicHubs - on <em>/search?search=<term>&genome=<name></em> function, restrict the search within the UCSC Genome Browser Public Hubs</li> <li>categories=trackDb - on <em>/search?search=<term>&genome=<name></em> function, restrict the search within the track database (trackDb) settings</li> </ul> </p> <p> The parameters are added to the endpoint URL beginning with a question mark <b>?</b>, and multiple parameters are separated with the semi-colon <b>;</b>. For example: <pre> https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM </pre> </p> <!-- ========== Required and optional parameters ======================= --> <a id="Parameter_use"></a> <h2>Required and optional parameters</h2> <p> <table> <tr><th>Endpoint function</th><th>Required</th><th>Optional</th></tr> +<tr><th>/findGenome</th><td>q</td><td>statsOnly, browser, year, category, status, level, maxItemsOutput</td></tr> <tr><th>/list/publicHubs</th><td>(none)</td><td>(none)</td></tr> <tr><th>/list/ucscGenomes</th><td>(none)</td><td>(none)</td></tr> <tr><th>/list/genarkGenomes</th><td>(none)</td><td>genome, maxItemsOutput</td></tr> <tr><th>/list/hubGenomes</th><td>hubUrl</td><td>(none)</td></tr> <tr><th>/list/files</th><td>genome</td><td>format=text, maxItemsOutput</td></tr> <tr><th>/list/tracks</th><td>genome or (hubUrl and genome)</td><td>trackLeavesOnly=1</td></tr> <tr><th>/list/chromosomes</th><td>genome or (hubUrl and genome)</td><td>track</td></tr> <tr><th>/list/schema</th><td>(genome or (hubUrl and genome)) and track</td><td>(none)</td></tr> <tr><th>/getData/sequence</th><td>(genome or (hubUrl and genome)) and chrom</td><td>start, end, revComp=1</td></tr> <tr><th>/getData/track</th><td>(genome or (hubUrl and genome)) and track</td><td>chrom, (start and end), maxItemsOutput, jsonOutputArrays</td></tr> <tr><th>/search</th><td>search and genome</td><td>categories=helpDocs, categories=publicHubs, categories=trackDb</td></tr> </table> </p> @@ -236,30 +244,39 @@ to the single specified chromosome. To limit the request to a specific position, both <b>start=4321</b> and <b>end=5678</b> must be given together. Using the <b>revComp=1</b> parameter returns the reverse complement. </p> <p> Use the <b>genome</b> argument with the <b>/list/genarkGenomes</b> function to test for the existence of a specific genome assembly in the <a href='https://hgdownload.soe.ucsc.edu/hubs/' target=_blank>Genark</a> set of assembly hubs. </p> <p> The <b>/list/files</b> endpoint only works for UCSC hosted genome assemblies, not for external hosted assembly hubs. </p> <p> +The <b>/findGenome</b> endpoint can find genome assemblies in the browser or +any other assembly available at NCBI even when not in the browser. Note, +there are almost 4 million assemblies available at NCBI. All searches are +<b>case insensitive</b>. Force inclusion: Use a + sign before <b>+word</b> to ensure +it appears in the result. Exclude words: Use a - sign before <b>-word</b> to +exclude it from the search result. Wildcard search: Add an * (asterisk) at +end of <b>word*</b> to search for all terms starting with that prefix. +</p> +<p> Any extra parameters not allowed in a function will be flagged as an error. </p> <!-- ========== Supported track types ======================= --> <a id="Track_types"></a> <h2>Supported track types for getData functions</h2> <div class="row"> <!-- Left column --> <div class="col-md-6"> <p> <ul> <li>altGraphX (e.g. 'sibTxGraph' for hg19)</li> <li><a href='/goldenPath/help/barChart.html' target=_blank>barChart/bigBarChart</a></li> <li><a href='/FAQ/FAQformat.html#format1' target=_blank>bed</a></li> <li><a href='/goldenPath/help/bigBed.html' target=_blank>bigBed</a></li> @@ -320,30 +337,38 @@ <b>https://genome-asia.ucsc.edu/cgi-bin/hubApi/list/ucscGenomes</b></li> </ul> <!-- ========== Example data access ======================= --> <a id="list_examples"></a> <h2>Example data access</h2> <p> Your WEB browser can be configured to interpret JSON data and format in a convenient browsing format. Firefox has this function built in, other browsers have add-ons that can be turned on to format JSON data. With your browser thus configured, the following links can demonstrate the functions of the API interface. </p> <h3>Listing functions</h3> <ol> +<li><a href='https://api.genome.ucsc.edu/findGenome?q=dog&jsonOutputArrays=1' target=_blank>find any genome with the word 'dog'</a> - +<b>api.genome.ucsc.edu/findGenome?q=dog</b></li> +<li><a href='https://api.genome.ucsc.edu/findGenome?q=%2Bwhite%20%2Brhino%2A%20-southern' target=_blank>find any genome matching the search string: '+white +rhino* -southern'</a> - +<b>api.genome.ucsc.edu/findGenome?q=%2Bwhite%20%2Brhino%2A%20-southern</b></li> +<li><a href='https://api.genome.ucsc.edu/findGenome?q=GCF_028858775.2' target=_blank>find any genome with the accession id: <b>GCF_028858775.2</b></a> - +<b>api.genome.ucsc.edu/findGenome?q=GCF_028858775.2</b></li> +<li><a href='https://api.genome.ucsc.edu/findGenome?q=GRCh38' target=_blank>find any genome with the name: <b>GRCh38</b></a> - +<b>api.genome.ucsc.edu/findGenome?q=GRCh38</b></li> <li><a href='https://api.genome.ucsc.edu/list/publicHubs' target=_blank>list public hubs</a> - <b>api.genome.ucsc.edu/list/publicHubs</b></li> <li><a href='https://api.genome.ucsc.edu/list/ucscGenomes' target=_blank>list UCSC database genomes</a> - <b>api.genome.ucsc.edu/list/ucscGenomes</b></li> <li><a href='https://api.genome.ucsc.edu/list/genarkGenomes?maxItemsOutput=5' target=_blank>list GenArk assembly hub genomes</a> - <b>api.genome.ucsc.edu/list/genarkGenomes?maxItemsOutput=5</b></li> <li><a href='https://api.genome.ucsc.edu/list/genarkGenomes?genome=GCF_028858775.2' target=_blank>test if genome GCF_028858775.2 exists in the GenArk assembly hub genomes</a> - <b>api.genome.ucsc.edu/list/genarkGenomes?genome=GCF_028858775.2</b></li> <li><a href='https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt' target=_blank>list genomes from specified hub</a> - <b>api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt</b></li> <li><a href='https://api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ' target=_blank>list tracks from specified hub and genome</a> - <b>api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ</b></li> <li><a href='https://api.genome.ucsc.edu/list/tracks?genome=hg38' target=_blank>list tracks from UCSC database genome</a> -