Thank you Brian. I tried the following command and did get the pdf version of the file, however I got all the tracks instead of just my user track,refseq track and base position track.
Here is the command I tried, I add the position myself so that I could automate the file creation process for a file of 10 co-ordinates. wget `wget -q " http://genome.ucsc.edu/cgi-bin/hgTracks?org=hg&db=hg19&position=chr9:21967752-219944&hgt.psOutput=on"; -O - | awk '/.pdf/ {gsub(".*HREF=\"..","",$3);gsub("\".*","",$3);print " http://genome.ucsc.edu/"; $3}'` -O checking.pdf" Are there other variables I need to set so that wget returns me the file just with the refseq track (pack) user uploaded track (dense) and base position (dense)? User uploaded track be shown in the pdf will be nice to have but not absolutely needed if that is difficult to do. Thanks again for all your help, Vinayak. On Wed, Jan 26, 2011 at 1:10 PM, Brian Raney <[email protected]> wrote: > 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 > > > > > -- -- "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
