Programmatic access to the Genome Browser: Difference between revisions

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* run a command like <code>bigWigToWig http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBroadHistoneK562Cbx2Sig.bigWig -chrom=chr21 -start=0 -end=10000000 stdout</code>. You can also replace stdout with a filename of your choice.
* run a command like <code>bigWigToWig http://hgdownload.cse.ucsc.edu/gbdb/hg19/bbi/wgEncodeBroadHistoneK562Cbx2Sig.bigWig -chrom=chr21 -start=0 -end=10000000 stdout</code>. You can also replace stdout with a filename of your choice.


* Download data stored in a database table
== Download data stored in a database table ==
** use Tools - Table Browser -  "Describe schema" to browse the database schema. All fields have a human readable description and the links to other tables are shown.
* use Tools - Table Browser -  "Describe schema" to browse the database schema. All fields have a human readable description and the links to other tables are shown.
** mysql --no-defaults -h genome-mysql.cse.ucsc.edu -u genome -A -e 'select * from pubsBingBlat' -NB > out.txt
* mysql --no-defaults -h genome-mysql.cse.ucsc.edu -u genome -A -e 'select * from pubsBingBlat' -NB > out.txt


* Get a copy of the current Genome Browser image from a script
== Get a copy of the current Genome Browser image from a script ==
**  use "curl http://genome.ucsc.edu/cgi-bin/hgRenderTracks > test.png". hgRenderTracks understands the same parameters and options as the main hgTracks CGI, e.g. <trackName>=pack.  
*  use "curl http://genome.ucsc.edu/cgi-bin/hgRenderTracks > test.png". hgRenderTracks understands the same parameters and options as the main hgTracks CGI, e.g. <trackName>=pack.  
**  to show only a single track with hgRenderTracks, make sure that the first track parameter is hideTracks=1
*  to show only a single track with hgRenderTracks, make sure that the first track parameter is hideTracks=1
** for example, to download the image for a chromosomal location with only the RefSeq transcripts and publications track to "pack" mode, use this command:
* for example, to download the image for a chromosomal location with only the RefSeq transcripts and publications track to "pack" mode, use this command:
   curl 'http://genome.ucsc.edu/cgi-bin/hgRenderTracks?position=chr17:41570860-41650551&hideTracks=1&refGene=pack&pubs=pack' > temp.png  
   <code>curl 'http://genome.ucsc.edu/cgi-bin/hgRenderTracks?position=chr17:41570860-41650551&hideTracks=1&refGene=pack&pubs=pack' > temp.png</code>


* Upload a custom track and link to the genome browser with the track loaded
== Upload a custom track and link to the genome browser with the track loaded ==
** create a custom track file as documented here http://genome.ucsc.edu/goldenpath/help/customTrack.html, e.g.: printf 'track name="TestTrack" description="TestTrack with links on features" url="http://www.google.com/$$"\nchr1 1 1000 testIdForUrl' > temp.bed
* create a custom track file as documented here http://genome.ucsc.edu/goldenpath/help/customTrack.html, e.g.: printf 'track name="TestTrack" description="TestTrack with links on features" url="http://www.google.com/$$"\nchr1 1 1000 testIdForUrl' > temp.bed
** upload your file with a command like this, it will print a string to stdout which we are calling $HGSID in the following <code>curl -s -F db=hg19 -F 'hgct_customText=@temp.bed' http://genome.ucsc.edu/cgi-bin/hgCustom  | grep -o 'hgsid=[0-9]*_[a-zA-Z0-9]*' | uniq | sed -e 's/hgsid=//'</code>
* upload your file with a command like this, it will print a string to stdout which we are calling $HGSID in the following <code>curl -s -F db=hg19 -F 'hgct_customText=@temp.bed' http://genome.ucsc.edu/cgi-bin/hgCustom  | grep -o 'hgsid=[0-9]*_[a-zA-Z0-9]*' | uniq | sed -e 's/hgsid=//'</code>
** you can link to a fresh genome browser session with only this track loaded with  http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=$HGSID&position=chr1:1-1000
* you can link to a fresh genome browser session with only this track loaded with  http://genome.ucsc.edu/cgi-bin/hgTracks?hgsid=$HGSID&position=chr1:1-1000
** you can load more tracks into this session by adding the parameter hgsid=$HGSID to all future curl calls
* you can load more tracks into this session by adding the parameter hgsid=$HGSID to all future curl calls
</ul>

Revision as of 09:35, 6 July 2015

The UCSC API for retrieving data and uploading data is not REST driven but revolves around client-side C tools that convert to/from binary files.

Here are some common tasks that can be solved with calls from scripts to the UCSC Genome Browser, assuming that you know the standard Unix command line tools:

Get the chromosome sequence for a range

Get the "wiggle" (x-y-plot) graph data for a chromosome range

Download data stored in a database table

  • use Tools - Table Browser - "Describe schema" to browse the database schema. All fields have a human readable description and the links to other tables are shown.
  • mysql --no-defaults -h genome-mysql.cse.ucsc.edu -u genome -A -e 'select * from pubsBingBlat' -NB > out.txt

Get a copy of the current Genome Browser image from a script

  • use "curl http://genome.ucsc.edu/cgi-bin/hgRenderTracks > test.png". hgRenderTracks understands the same parameters and options as the main hgTracks CGI, e.g. <trackName>=pack.
  • to show only a single track with hgRenderTracks, make sure that the first track parameter is hideTracks=1
  • for example, to download the image for a chromosomal location with only the RefSeq transcripts and publications track to "pack" mode, use this command:
  curl 'http://genome.ucsc.edu/cgi-bin/hgRenderTracks?position=chr17:41570860-41650551&hideTracks=1&refGene=pack&pubs=pack' > temp.png

Upload a custom track and link to the genome browser with the track loaded

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