3d50e0f18a7c64a85cd2dce1440f59ab0ee08ed7 hiram Tue May 14 21:54:51 2019 -0700 until this page becomes smart with js make the examples go explicitly to api.genome.ucsc.edu refs #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index ff661df..7efa326 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -173,99 +173,99 @@

Example data access

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.

Listing functions

    -
  1. list public hubs - +
  2. list public hubs - api.genome.ucsc.edu/list/publicHubs
    3. -
  3. list UCSC database genomes - +
  4. list UCSC database genomes - api.genome.ucsc.edu/list/ucscGenomes
    5. -
  5. list genomes from specified hub - api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt
    6. -
  6. list tracks from specified hub and genome - api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
    7. -
  7. list tracks from UCSC database genome - +
  8. list tracks from UCSC database genome - api.genome.ucsc.edu/list/tracks?genome=ce11
    9. -
  9. list chromosomes from UCSC database genome - +
  10. list chromosomes from UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=ce11
    11. -
  11. list chromosomes from specified track in UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold
    12. -
  12. list chromosomes from assembly hub genome -
    api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
    13. -
  13. list chromosomes from specified track in assembly hub genome -
    api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly

getData functions

    -
  1. Get DNA sequence from specified chromosome in UCSC database genome -
    api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM
    2. -
  2. Get DNA sequence from specified chromosome and start,end coordinates in UCSC database genome -
    api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM;start=4321;end=5678
    3. -
  3. Get DNA sequence from a track hub where 'genome' is a UCSC database -
    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
    4. -
  4. Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome -
    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
    5. -
  5. Get track data for specified track in UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100
    6. -
  6. Get track data for specified track and chromosome in UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrM
    7. -
  7. Get track data for specified track, chromosome and start,end coordinates in UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrI;start=47000;end=48000
    8. -
  8. Get track data for specified track in an assembly hub genome -
    api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly
    9. -
  9. Get track data for specified track and chromosome in an assembly hub genome -
    api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly;chrom=chrCp
    10. -
  10. Get track data for specified track in a track hub -
    api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved
    11. -
  11. Get track data for specified track and chromosome in a track hub -
    api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/GillBejerano/hub.txt;genome=hg19;track=ultraConserved;chrom=chr8
    12. -
  12. Wiggle track data for specified track, chromosome with start and end limits in an assembly hub genome -
    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
    13. -
  13. Wiggle track data for specified track in a UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100
    14. -
  14. bigBed data from a UCSC database, chrom and start,end limits -
    api.genome.ucsc.edu/getData/track?genome=galGal6;track=ncbiRefSeqOther;chrom=chr1;start=750000;end=55700000

Error return examples

    -
  1. Request track data for non-existent chromosome in an assembly hub genome -
    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