4394637e2f1a5665405d2a70cde01e0c9bea18ca hiram Tue May 7 13:05:22 2019 -0700 eliminate underscores from Plants hub names refs #18869 diff --git src/hg/htdocs/goldenPath/help/api.html src/hg/htdocs/goldenPath/help/api.html index 5111363..0ab8603 100755 --- src/hg/htdocs/goldenPath/help/api.html +++ src/hg/htdocs/goldenPath/help/api.html @@ -180,92 +180,92 @@ 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 - api.genome.ucsc.edu/list/publicHubs
  2. list UCSC database genomes - api.genome.ucsc.edu/list/ucscGenomes
  3. list genomes from specified hub - api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt
    4. -
  4. 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
    5. +api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
  5. list tracks from UCSC database genome - api.genome.ucsc.edu/list/tracks?genome=ce11
  6. list chromosomes from UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=ce11
  7. list chromosomes from specified track in UCSC database genome - api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold
    8. -
  8. 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
    9. -
  9. api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
    10. +
  10. 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_
    11. +
    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. 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. 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. +
    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. Get track data for specified track in UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100
  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. 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. api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly
    10. +
  10. 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
    11. +
    api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly;chrom=chrCp
  11. 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
  12. 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
    13. -
  13. 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
    14. +
    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
  14. Wiggle track data for specified track in a UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100
  15. 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
    2. +
    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