# UCSC fetch

A script to fetch screenshots from the UCSC browser

## Usage:

\$: python fetch_ucsc.py --regions <regions file> --tracks <tracks file> --browser_config <browser config file> [--output-folder <output folder>]

In order to use this script, you need to edit and customize three files: the Regions file, the Tracks file, and the Browser config file. Most of these have default values included in this distribution, but be sure to change your email address in the Browser config file, otherwise the script will refuse to work.

### 1. the Regions file

The regions file is a tab-separated file containing the regions to be displayed, one per line. The script will generate a separate .pdf file for each entry in this file.

Example:

#label, organism, assembly, chromosome, start, end, description, upstream, downstream
IL10, human, hg18, chr1, 205007571, 205012462, "involved in immunity", 10000, 1000
PRNP, human, hg18, chr20, 4615157, 4630234, "Prion Protein", 10000, 10000
HSPB4, human, hg18, chr21, 43462210, 43465982, "Heat-shock protein", 10000, 10000


Look at params/regions/default.txt for an example Regions file.

### 2. the Tracks file

The tracks file contains the configuration of which tracks to show, and of which database and organism to use. For each entry in the Regions file, the script will generate a pdf with the same tracks for each.

Example:

[visual_options]

[custom_tracks]
track1 = http://pastebin.com/raw.php?i=CKCuYGmX

[tracks]
wgRna=hide
wgEncodeReg=hide
cpgIslandExt=hide
ensGene=hide
mrna=hide
intronEst=hide
mgcGenes=hide
cons44way=hide
snp130=hide
snpArray=hide
refGene=hide
wgEncodeRegMarkPromoter=full
knownGene=full
rmsk=hide
phyloP46wayPlacental=hide


Or save visual settings (track height, mode, or track data from track hubs, etc.) as session, and set as shared. See example figure 'reports/session1_session1_default.pdf' from calling fetch_ucsc.py with parameters "-r params/regions/session1.txt -t params/tracks_options/session1.txt".

Example:

[session]
UserSessionName=hg19SessionEx1


Look at params/tracks_options/default.txt for an example Regions file.

### 3. the Browser config file

You can change the UCSC URL to point to a custom UCSC browser installation, if you have.

It is important to define an email address. This will be shown in the log files of the UCSC server, and will be used by UCSC administrators in case they need to contact you about usage policy. Be careful not to exceed with the queries, as this may create problems to other users of the UCSC browser.

Example:

[browser]
ucsc_base_url = http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg18