43156046fa4f7e34065194cb742ec39a4a7334e2 lrnassar Wed May 15 10:44:07 2019 -0700 Switching examples from plant to mouse hub and switching ce11 or hg38 #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 7efa326..092787e 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -177,95 +177,95 @@ <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> -<li><a href='https://api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt' +<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://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt</b></li> -<li><a href='https://api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1' +<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://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1</b></li> -<li><a href='https://api.genome.ucsc.edu/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='https://api.genome.ucsc.edu/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='https://api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold' +<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=ce11;track=gold</b></li> -<li><a href='https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1' +<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> - -<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='https://api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly' +<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ</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;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> +<br><b>api.genome.ucsc.edu/list/chromosomes?hubUrl=hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly</b></li> </ol> <a id="getData_examples"></a> <h3>getData functions</h3> <ol> -<li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM' +<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=ce11;chrom=chrM</b></li> -<li><a href='https://api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM;start=4321;end=5678' +<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=ce11;chrom=chrM;start=4321;end=5678</b></li> -<li><a href='https://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' +<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?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://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;chrom=chrM;start=4321;end=5678</b></li> -<li><a href='https://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' -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='https://api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100' +<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=ce11;track=gold;maxItemsOutput=100</b></li> -<li><a href='https://api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrM' +<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=ce11;track=gold;chrom=chrM</b></li> -<li><a href='https://api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrI;start=47000;end=48000' +<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=ce11;track=gold;chrom=chrI;start=47000;end=48000</b></li> -<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly' +<br><b>api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;start=47000;end=48000</b></li> +<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;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> +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly</b></li> <li><a href='https://api.genome.ucsc.edu/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='https://api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved' +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chr1</b></li> +<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene' 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='https://api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8' +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene</b></li> +<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene;chrom=chr1' 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='https://api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=gc5Base;chrom=chrCp;start=4321;end=5678' +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene;chrom=chr1</b></li> +<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=gc5Base;chrom=chr1;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> +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=gc5Base;chrom=chr1;start=4321;end=5678</b></li> <li><a href='https://api.genome.ucsc.edu/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='https://api.genome.ucsc.edu/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 id="Error_examples"></a> <h3>Error return examples</h3> <p> <ol> -<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=gc5Base;chrom=chrI;start=4321;end=5678' +<li><a href='https://api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chrI;start=43521;end=54321' 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> +<br><b>api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chrI;start=43521;end=54321</b></li> </ol> </p> <!--#include virtual="$ROOT/inc/gbPageEnd.html" -->