b0d399498f44f25274a920db635078590582230e gperez2 Tue Jul 2 15:18:44 2024 -0700 Adding documentation and an example for getting the reverse complement sequence using the API, refs #26691 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 188a380..0b3c991 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -112,30 +112,32 @@ <p> <ul> <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</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 - return reverse complement of sequence data (chrom, start, and end required + together)</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>trackLeavesOnly=1 - on <em>/list/tracks</em> function, only show tracks, do not show composite container information</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 @@ -152,49 +154,50 @@ </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> <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 and -end</td></tr> +<tr><th>/getData/sequence</th><td>(genome or (hubUrl and genome)) and chrom</td><td>start, end, and +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> <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> <p> <ul> <li><a href='/FAQ/FAQformat.html#format21' target=_blank>barChart</a></li> @@ -282,30 +285,33 @@ target=_blank>list download files for UCSC GenArk genome 'GCF_000955945.1' in JSON format limit 5 items output</a> - <br><b>api.genome.ucsc.edu/list/files?genome=GCF_000955945.1;maxItemsOutput=5</b></li> <li><a href='https://api.genome.ucsc.edu/list/files?genome=hs1;format=text;maxItemsOutput=5' target=_blank>list download files for UCSC genome 'hs1' in plain text format limit 5 items output</a> - <br><b>api.genome.ucsc.edu/list/files?genome=hs1;format=text;maxItemsOutput=5</b></li> </ol> <a id="getData_examples"></a> <h3>getData functions</h3> <ol> <li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678</b></li> +<li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678;revComp=1' +target=_blank>Get the reverse complement of the DNA sequence from specified chromosome and start,end coordinates in UCSC database genome</a> - +<br><b>api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678;revComp=1</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=mm10;chrom=chrM;start=4321;end=5678' target=_blank>Get DNA sequence from a track hub where 'genome' is a UCSC database</a> - <br><b>api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=mm10;chrom=chrM;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;chrom=chr1;start=4321;end=5678' target=_blank>Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome</a> - <br><b>api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;chrom=chr1;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;maxItemsOutput=100' target=_blank>Get track data for specified track in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;maxItemsOutput=100</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chrM' target=_blank>Get track data for specified track and chromosome in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chrM</b></li> <li><a href='https://api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;start=47000;end=48000' target=_blank>Get track data for specified track, chromosome and start,end coordinates in UCSC database genome</a> - <br><b>api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;start=47000;end=48000</b></li>