Hey Vinayak, Thanks for your question.
We do not have much support for using the Genome Browser as a background service. To do this efficiently, you'd want to maintain a set of cookies (or cart) with the settings of the tracks you want to display. We keep track of the cart through the "hgsid" CGI variable. We're working on a document that describes how to use the hgsid variable, but for now you should be able to scrape it out the HTML that our hgTracks program generates. We have a little bit of instruction on how to use CGI variables to control hgTracks here: http://genome.ucsc.edu/FAQ/FAQlink.html To generate a PDF file automatically, you'll also need to do some scraping of the HTML from hgTracks to find the PDF file name after passing the CGI variable "hgt.psOutput=on" to hgTracks. I've included a little script that demonstrates a simple mechanism to ask hgTracks to generate a PDF file, then to grab the PDF file that is mentioned in the HTML. wget `wget -q "http://genome.ucsc.edu/cgi-bin/hgTracks?hgt.psOutput=on"; -O - | awk '/.pdf/ {gsub(".*HREF=\"..","",$3);gsub("\".*","",$3);print "http://genome.ucsc.edu/"; $3}'` -O my.pdf I hope this gets you started. Please respond to this list if you have more questions. Brian On Mon, Jan 24, 2011 at 3:16 PM, Vinayak Kulkarni <[email protected]> wrote: > Dear UCSC folks, > I have bed tracks loaded in UCSC and was wondering if there is an automated > way to create the pdf pictures that one can create using UCSC page? > Attached is the image for your perusal. > Thank you very much, > Vinayak. > > -- > -- > "Hesitating to act because the whole vision might not be achieved, or > because others do not yet share it, is an attitude that only hinders > progress"... Mahatma Gandhi > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
