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 @@

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 - api.genome.ucsc.edu/list/publicHubs
  2. list UCSC database genomes - api.genome.ucsc.edu/list/ucscGenomes
    3. -
  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. api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt
    5. +
  5. 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
    6. -
  6. list tracks from UCSC database genome - -api.genome.ucsc.edu/list/tracks?genome=ce11
    7. -
  7. list chromosomes from UCSC database genome - -api.genome.ucsc.edu/list/chromosomes?genome=ce11
    8. -
  8. api.genome.ucsc.edu/list/tracks?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
    9. +
  9. list tracks from UCSC database genome - +api.genome.ucsc.edu/list/tracks?genome=hg38
    10. +
  10. list chromosomes from UCSC database genome - +api.genome.ucsc.edu/list/chromosomes?genome=hg38
    11. +
  11. list chromosomes from specified track in UCSC database genome - -api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold
    12. -
  12. api.genome.ucsc.edu/list/chromosomes?genome=hg38;track=gold
    13. +
  13. 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
    14. -
  14. api.genome.ucsc.edu/list/chromosomes?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ
    15. +
  15. 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
    16. +
    api.genome.ucsc.edu/list/chromosomes?hubUrl=hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;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. api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM
    3. +
  3. 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
    4. -
  4. api.genome.ucsc.edu/getData/sequence?genome=hg38;chrom=chrM;start=4321;end=5678
    5. +
  5. 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
    6. -
  6. 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
    7. -
  7. api.genome.ucsc.edu/getData/sequence?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=mm10;chrom=chrM;start=4321;end=5678
    8. +
  8. Get DNA sequence from specified chromosome and start,end coordinates in an assembly hub genome - +
    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
    9. +
  9. Get track data for specified track in UCSC database genome - -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100
    10. -
  10. api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;maxItemsOutput=100
    11. +
  11. Get track data for specified track and chromosome in UCSC database genome - -
    api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrM
    12. -
  12. api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chrM
    13. +
  13. 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
    14. -
  14. api.genome.ucsc.edu/getData/track?genome=hg38;track=gold;chrom=chr1;start=47000;end=48000
    15. +
  15. 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
    16. +
    api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly
  16. 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
    17. -
  17. api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chr1
    18. +
  18. 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
    19. -
  19. api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene
    20. +
  20. 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
    21. -
  21. api.genome.ucsc.edu/getData/track?hubUrl=http://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=ensGene;chrom=chr1
    22. +
  22. 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
    23. +
    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
  23. Wiggle track data for specified track in a UCSC database genome -
    api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100
  24. 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://hgdownload.soe.ucsc.edu/hubs/mouseStrains/hub.txt;genome=CAST_EiJ;track=assembly;chrom=chrI;start=43521;end=54321