The GREAT Programming Interface allows external clients to submit BED data automatically for analysis by GREAT and display in the GREAT user interface. For example, it is used by the UCSC Table Browser to send data to GREAT. Anyone is welcome to use the interface, and we particularly encourage genome browser portals and ChIP-seq peak calling tools to integrate with GREAT through the GREAT Programming Interface.
To submit BED data for analysis by GREAT, a client sends an HTTP GET request to http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php
that includes:
requestURL
(required) - The URL for the BED data to process.requestSpecies
(required) - The species assembly (e.g. hg18) corresponding to the BED data.requestName
(optional) - The name used to identify the BED data on the GREAT output page. If not given, "external data" is used.requestSender
(optional) - The name of the tool submitting the data, which is used as a prefix to requestName
to identify the data on the GREAT output page.bgURL
(optional) - The URL for the BED data used as the background for the foreground/background test.bgName
(optional) - The name used to identify the background BED data on the GREAT output page. If not given, "external background data" is used.outputType
(optional) - The mode in which GREAT returns output.web
" - the standard GREAT UI for presentation in a browser (best for linking from an external website to GREAT)batch
" - a tab separated file for machine processing (best for script-powered analyses)Submitting an HTTP GET request to GREAT is as simple as including the necessary parameters in a URL link (see examples).
As written inĀ GREAT bulk access limits, please limit your GREAT jobs to 1 job per 60 seconds.
requestURL
When GREAT receives a request, it in turn retrieves the BED data at the requestURL
via HTTP GET. The requestURL
must point to either a BED file or a script that generates BED data (see examples).
requestURL
should be HTTP encoded so that it is safe to pass via GET (see examples). To encode a URL, enter it at the URL Decoder/Encoder and choose "Encode."The data submitted to GREAT must be valid BED format as used with the UCSC Genome Browser. Lines that start with "#" are considered comments and are ignored. Compressed data is supported.
Batch mode returns a tab-separated text file with GREAT statistical test results for your input data set.
In the first example, the client has a BED file available on its server (at http://www.clientA.com/data/example1.bed) that it wishes for GREAT to process.
*http://www.clientA.com/data/example1.bed:*
# SRF example data chr5 60663738 60663788 SRF.1 chr5 137828954 137829004 SRF.2 chr5 137828665 137828715 SRF.3 chr7 5536799 5536849 SRF.4 |
To submit this data to GREAT, the client webpage includes a link that sends an HTTP GET request to GREAT. When the link is clicked, the request is sent to GREAT:
<html> <body> <a href="http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php?requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed"> Send to GREAT </a> </body> </html> |
In the second example, the client has a script (at http://www.clientB.com/data/example2.php) that generates BED data for GREAT to process.
*http://www.clientB.com/data/example2.php:*
<?php if ($_GET["tf"] == "Srf") { echo "chr5 60663738 60663788 SRF.1\n"; echo "chr5 137828954 137829004 SRF.2\n"; echo "chr5 137828665 137828715 SRF.3\n"; echo "chr7 5536799 5536849 SRF.4\n"; } else if ($_GET["tf"] == "Nrsf") { echo "chr1 11017025 11017401 NRSF.1\n"; echo "chr6 12605475 12606176 NRSF.2\n"; echo "chr8 12680375 12681376 NRSF.3\n"; echo "chr4 13416275 13416776 NRSF.4\n"; } ?> |
Again, to submit this data to GREAT, the client webpage includes a link that sends an HTTP GET request to GREAT. The requestURL
in turn includes information for GREAT to submit an HTTP GET request back to the client to obtain the BED data:
<html> <body> <a href="http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php?requestSpecies=hg18&requestURL=http%3A%2F%2Fwww.clientB.com%2Fdata%2Fexample2.php%3Ftf%3DNrsf"> Send NRSF data to GREAT </a> </body> </html> |
In the first example, the client has a BED file available on its server (at http://www.clientA.com/data/example1.bed) that it wishes for GREAT to process. The client wants to do further automated processing, and thus wishes to have the GREAT results in a machine-readable tab-separated format.
*http://www.clientA.com/data/example1.bed:*
# SRF example data chr5 60663738 60663788 SRF.1 chr5 137828954 137829004 SRF.2 chr5 137828665 137828715 SRF.3 chr7 5536799 5536849 SRF.4 |
To submit this data to GREAT, the client issues a "wget" request and specifies "outputType=batch
":
wget -O results.tsv "http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed" |
The GREAT server currently accepts a maximum of 5 API requests for all API users at any given time. More than 5 requests will be denied. To make the maximum of 5 API calls
you will need to split your jobs and process them separately. A possibly way of processing the data is seen in our greatBatchQuery.py script. Feel free to adapt it to your needs.
How does greatBatchQuery.py work?
outputFile queryURL
where each line is a new jobEX:
results1.tsv http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample1.bed results2.tsv http://bejerano.stanford.edu/great/public/cgi-bin/greatStart.php?outputType=batch&requestSpecies=hg18&requestName=Example+Data&requestSender=Client+A&requestURL=http%3A%2F%2Fwww.clientA.com%2Fdata%2Fexample2.bed |
./greatBatchQuery.py joblist