1a3c324b528c57e4b6211d872a3b4e666b032259 jnavarr5 Mon Apr 14 16:27:03 2025 -0700 Adding function for listing GenArk genomes, refs #32897 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 743f10d5733..11e3c49ccc5 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -199,66 +199,62 @@ 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>/list/publicHubs</th><td>(none)</td><td>(none)</td></tr> <tr><th>/list/ucscGenomes</th><td>(none)</td><td>(none)</td></tr> -<!-- not yet <tr><th>/list/genarkGenomes</th><td>(none)</td><td>genome</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> <p> The <b>hubUrl</b> and <b>genome</b> parameters are required together to specify a unique genome in an assembly or track hub. The <b>genome</b> for a track hub will usually be a UCSC database genome. Assembly hubs will have their own unique <b>genome</b> sequences. Specify <b>genome</b> without a <b>hubUrl</b> to refer to a UCSC Genome Browser assembly. </p> <p> Using the <b>chrom=<name></b> parameter will limit the request 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> -<!-- not yet <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> 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> @@ -327,36 +323,34 @@ <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/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> -<!-- not yet -<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/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> - <b>api.genome.ucsc.edu/list/tracks?genome=hg38</b></li> <li><a href='https://api.genome.ucsc.edu/list/chromosomes?genome=hg38' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=hg38</b></li> <li><a href='https://api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold</b></li> <li><a href='https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ' target=_blank>list chromosomes from assembly hub genome</a> -