438e3f1d32b858255405c7bb3fccb7190d06fca1 hiram Sun Apr 28 13:12:25 2019 -0700 eliminating the db= argument everywhere, only need genome= refs #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 413bf32..b52332a 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -75,75 +75,71 @@ <li><b>/list/ucscGenomes</b> - list UCSC database genomes</li> <li><b>/list/hubGenomes</b> - list genomes from specified hub</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 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> </ul> </p> <!-- ========== Parameters to endpoint functions ======================= --> <a name="Parameters"></a> <h2>Parameters to endpoint functions</h2> <p> <ul> <li>hubUrl=<url> - specify track hub or assembly hub URL</li> -<li>genome=<name> - specify genome assemby in track or assembly hub (only used with hubUrl)</li> -<li>db=<ucscDb> - specify database (aka genome assembly) in UCSC genome browser (either hubUrl or db specified, not both)</li> +<li>genome=<name> - specify genome assembly in UCSC genome browser, track or assembly hub</li> <li>track=<trackName> - specify data track in 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)</li> <li>end=<456> - specify end coordinate (1 relative) for data from track or sequence retrieval (start and end required together)</li> <li>(see also: <a href='http://genome.ucsc.edu/blog/the-ucsc-genome-browser-coordinate-counting-systems/' target=_blank>UCSC browser coordinate counting systems)</a></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 </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-test.gi.ucsc.edu/getData/sequence?db=ce11;chrom=chrM +https://api-test.gi.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM </pre> </p> <!-- ========== Required and optional parameters ======================= --> <a name="Parameter use"></a> <h2>Required and optional parameters</h2> <p> <table border=1> <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/tracks</th><td>(hubUrl and genome) or db</td><td>trackLeavesOnly=1</td></tr> -<tr><th>/list/chromosomes</th><td>((hubUrl and genome) or db) and track</td><td>(none)</td></tr> -<tr><th>/getData/sequence</th><td>((hubUrl and genome) or db) and chrom</td><td>start and end</td></tr> -<tr><th>/getData/track</th><td>((hubUrl and genome) or db) and track</td><td>chrom, (start and end), maxItemsOutput, jsonOutputArrays</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>/getData/sequence</th><td>(genome or (hubUrl and genome)) and chrom</td><td>start and end</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> </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. -</p> -<p> -When not an assembly or track hub, to access UCSC database assemblies, -the parameter <b>db=<name></b> is required. +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. </p> <!-- ========== Supported track types ======================= --> <a name="Track types"></a> <h2>Supported track types, at this time (April 2019), for getData functions</h2> <p> <ul> <li><a href='/FAQ/FAQformat.html#format1' target=_blank>bed</a></li> <li><a href='/FAQ/FAQformat.html#format1.5' target=_blank>bigBed</a></li> <!-- not yet @@ -157,51 +153,51 @@ <li><a href='http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/rmsk.sql' target=_blank>rmsk - repeat masker</li> <li><a href='/FAQ/FAQformat.html#format6' target=_blank>wig</a></li> <li>(Work is under way to support additional track types)</li> </ul> </p> <!-- ========== Example data access ======================= --> <a name="list examples"></a> <h2>Example data access</h2> <h3>Listing functions</h3> <ol> <li><a href='/list/publicHubs' target=_blank>list public hubs</a> - <b>api.genome.ucsc.edu/list/publicHubs</b></li> <li><a href='/list/ucscGenomes' target=_blank>list UCSC database genomes</a> - <b>api.genome.ucsc.edu/list/ucscGenomes</b></li> <li><a href='/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt' target=_blank>list genomes from specified hub</a> - <b>api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt</b></li> <li><a href='/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list tracks from specified hub and genome</a> - <b>api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li> -<li><a href='/list/tracks?db=ce11' target=_blank>list tracks from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/tracks?db=ce11</b></li> -<li><a href='/list/chromosomes?db=ce11' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11</b></li> -<li><a href='/list/chromosomes?db=ce11;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?db=ce11;track=gold</b></li> +<li><a href='/list/tracks?genome=ce11' target=_blank>list tracks from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/tracks?genome=ce11</b></li> +<li><a href='/list/chromosomes?genome=ce11' target=_blank>list chromosomes from UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=ce11</b></li> +<li><a href='/list/chromosomes?genome=ce11;track=gold' target=_blank>list chromosomes from specified track in UCSC database genome</a> - <b>api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold</b></li> <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1' target=_blank>list chromosomes from assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1</b></li> <li><a href='/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>list chromosomes from specified track in assembly hub genome</a> -<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li> </ol> <a name="getData examples"></a> <h3>getData functions</h3> <ol> -<li><a href='/getData/sequence?db=ce11;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?db=ce11;chrom=chrM</b></li> -<li><a href='/getData/sequence?db=ce11;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?db=ce11;chrom=chrM;start=4321;end=5678</b></li> +<li><a href='/getData/sequence?genome=ce11;chrom=chrM' target=_blank>Get DNA sequence from specified chromosome in UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM</b></li> +<li><a href='/getData/sequence?genome=ce11;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=ce11;chrom=chrM;start=4321;end=5678</b></li> <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;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://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678</b></li> <li><a href='/getData/sequence?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678' target=_blank><b></b> 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://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;chrom=chrCp;start=4321;end=5678</b></li> -<li><a href='/getData/track?db=ce11;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?db=ce11;track=gold;maxItemsOutput=100</b></li> -<li><a href='/getData/track?db=ce11;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?db=ce11;track=gold;chrom=chrM</b></li> -<li><a href='/getData/track?db=ce11;track=gold;chrom=chrI;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?db=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li> +<li><a href='/getData/track?genome=ce11;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=ce11;track=gold;maxItemsOutput=100</b></li> +<li><a href='/getData/track?genome=ce11;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=ce11;track=gold;chrom=chrM</b></li> +<li><a href='/getData/track?genome=ce11;track=gold;chrom=chrI;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=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_' target=_blank>Get track data for specified track in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp' target=_blank>Get track data for specified track and chromosome in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved' target=_blank>Get track data for specified track in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8' target=_blank>Get track data for specified track and chromosome in a track hub</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8</b></li> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrCp;start=4321;end=5678' target=_blank>Wiggle track data for specified track, chromosome with start and end limits in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrCp;start=4321;end=5678</b></li> -<li><a href='/getData/track?db=galGal6;track=gc5BaseBw;maxItemsOutput=100' target=_blank>Wiggle track data for specified track in a UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100</b></li> -<li><a href='/getData/track?db=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000' target=_blank>bigBed data from a UCSC database, chrom and start,end limits</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000</b></li> +<li><a href='/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100' target=_blank>Wiggle track data for specified track in a UCSC database genome</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100</b></li> +<li><a href='/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000' target=_blank>bigBed data from a UCSC database, chrom and start,end limits</a> -<br><b>api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000</b></li> </ol> <p> </p> <a name="Error examples"></a> <h3>Error return examples</h3> <p> <ol> <li><a href='/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=gc5Base_;chrom=chrI;start=4321;end=5678' target=_blank>Request track data for non-existent chromosome in an assembly hub genome</a> -<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=_araTha1;track=assembly_;chrom=chrI;start=43521;end=54321</b></li> </ol> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->