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
@@ -1,271 +1,271 @@
JSON API data interface
Contents
What is JSON data ?
JSON data is a data transfer syntax from a data provider to a data consumer.
See also: JSON Introduction
What is the access URL ?
This access url: https://api.genome.ucsc.edu/ is used to access
the endpoint functions. For example:
wget -O- 'https://api.genome.ucsc.edu/list/publicHubs'
What type of data can be accessed ?
The following data sets can be accessed at this time:
- List of available public hubs
- List of available UCSC Genome Browser genome assemblies
- List genomes from a specified assembly or track hub
- List available data tracks from a specified hub or UCSC Genome Browser genome assembly
(see also: track definition help)
- List of chromosomes contained in an assembly hub or UCSC Genome Browser genome assembly
- List of chromosomes contained in a specific track of an assembly or track hub, or UCSC Genome
Browser genome assembly
- Return DNA sequence from an assembly hub 2bit file, or UCSC Genome Browser assembly
- Return track data from a specified assembly or track hub, or UCSC Genome Browser assembly
Endpoint functions to return data
The url https://api.genome.ucsc.edu/ is used to access
the endpoint functions. For example:
wget -O- 'https://api.genome.ucsc.edu/list/publicHubs'
- /list/publicHubs - list public hubs
- /list/ucscGenomes - list UCSC Genome Browser database genomes
- /list/hubGenomes - list genomes from specified hub
- /list/tracks - list data tracks available in specified hub or database genome
(see also: track definition help)
- /list/chromosomes - list chromosomes from a data track in specified hub or database
genome
- /getData/sequence - return sequence from specified hub or database genome
- /getData/track - return data from specified track in hub or database genome
Parameters to endpoint functions
- hubUrl=<url> - specify track hub or assembly hub URL
- genome=<name> - specify genome assembly in UCSC Genome Browser or track/assembly hub
- track=<trackName> - specify data track in track/assembly hub or UCSC database genome
assembly
- chrom=<chrN> - specify chromosome name for sequence or track data
- start=<123> - specify start coordinate (0 relative) for data from track or sequence
retrieval (start and end required together). See also: UCSC browser coordinate counting systems
- end=<456> - specify end coordinate (1 relative) for data from track or sequence
retrieval (start and end required together). See also: UCSC browser coordinate counting systems
- maxItemsOutput=1000 - limit number of items to output, default: 1,000, maximum limit:
1,000,000 (use -1 to get maximum output)
- trackLeavesOnly=1 - on /list/tracks function, only show tracks, do not show
composite container information
- jsonOutputArrays=1 - on /getData/track function, JSON format is array type
for each item of data, instead of the default object type
The parameters are added to the endpoint URL beginning with a
question mark ?, and multiple parameters are separated with
the semi-colon ;. For example:
https://api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM
Required and optional parameters
| Endpoint function | Required | Optional |
|---|
| /list/publicHubs | (none) | (none) |
|---|
| /list/ucscGenomes | (none) | (none) |
|---|
| /list/hubGenomes | hubUrl | (none) |
|---|
| /list/tracks | genome or (hubUrl and genome) | trackLeavesOnly=1 |
|---|
| /list/chromosomes | genome or (hubUrl and genome) | track |
|---|
| /getData/sequence | (genome or (hubUrl and genome)) and chrom | start and
end |
|---|
| /getData/track | (genome or (hubUrl and genome)) and track | chrom,
(start and end), maxItemsOutput, jsonOutputArrays |
|---|
The hubUrl and genome parameters are required together to
specify a unique genome in an assembly or track hub. The genome for
a track hub will usually be a UCSC database genome. Assembly hubs will
have their own unique genome sequences. Specify genome without
a hubUrl to refer to a UCSC Genome Browser assembly.
Using the chrom=<name> parameter will limit the request
to the single specified chromosome. To limit the request to a specific
position, both start=4321 and end=5678 must be given together.
Any extra parameters not allowed in a function will be flagged as an error.
Supported track types, at this time (April 2019), for getData functions
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
- list public hubs -
api.genome.ucsc.edu/list/publicHubs
- list UCSC database genomes -
api.genome.ucsc.edu/list/ucscGenomes
- list genomes from specified hub -
api.genome.ucsc.edu/list/hubGenomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt
-- 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
+api.genome.ucsc.edu/list/tracks?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
- list tracks from UCSC database genome -
api.genome.ucsc.edu/list/tracks?genome=ce11
- list chromosomes from UCSC database genome -
api.genome.ucsc.edu/list/chromosomes?genome=ce11
- list chromosomes from specified track in UCSC database genome -
api.genome.ucsc.edu/list/chromosomes?genome=ce11;track=gold
-- 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
-- api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1
+- 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_
+
api.genome.ucsc.edu/list/chromosomes?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly
getData functions
- Get DNA sequence from specified chromosome in UCSC database genome -
api.genome.ucsc.edu/getData/sequence?genome=ce11;chrom=chrM
- 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
- 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
-- 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
+
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
- Get track data for specified track in UCSC database genome -
api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;maxItemsOutput=100
- Get track data for specified track and chromosome in UCSC database genome -
api.genome.ucsc.edu/getData/track?genome=ce11;track=gold;chrom=chrM
- 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
-- 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_
-- api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly
+- 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
+
api.genome.ucsc.edu/getData/track?hubUrl=http://genome-test.gi.ucsc.edu/~hiram/hubs/Plants/hub.txt;genome=araTha1;track=assembly;chrom=chrCp
- 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
- 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
-- 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
+
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
- Wiggle track data for specified track in a UCSC database genome -
api.genome.ucsc.edu/getData/track?genome=galGal6;track=gc5BaseBw;maxItemsOutput=100
- 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
-- 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
+
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