Hello Mark, One of our engineers suggested using the Session feature in conjunction with command-line hgTracks. You could do something like this:
1. Save a session (using the "Session" link in the blue bar at the top of the page) with the desired tracks and settings turned on. 2. Copy the "Browser" link from the session page, and translate the URL into a command-line invocation by running $CGI-BIN/hgTracks with the stuff that appears after the "?" in the URL, plus a position range, all single-quoted. e.g.: /usr/local/bin/hgTracks 'hgSs_otherUser=me&hgSs_....&position=chr1:2-3' > chr1:2-3.html 3. Then scrape the image filename from the html file and rename it to something that indicates the position range. I hope this helps. Please contact us again at [email protected] <mailto:[email protected]> if you have further questions. Best, Antonio Coelho UCSC Genome Bioinformatics Group Miller, Mark A. wrote: > I would like to extract images of a few hundred genomic regions for one > of the organisms hosted at Merck's instance of the USCS browser. I > definitely don't want to type the coordinates or a locus name into the > search box and then save the image from my web browser hundreds of > times. I am exploring wget or curl, but that may be a pain because > Merck's UCSC browser is pass word protected, and I don't understand what > authentication protocol they are using. > > Can you suggestion any method for scraping images from the USCS genome > browser, with specified tracks, for specified regions, in a hands-off > manner? > > Thanks, > Mark > > Notice: This e-mail message, together with any attachments, contains > information of Merck & Co., Inc. (One Merck Drive, Whitehouse Station, > New Jersey, USA 08889), and/or its affiliates Direct contact information > for affiliates is available at > http://www.merck.com/contact/contacts.html) that may be confidential, > proprietary copyrighted and/or legally privileged. It is intended solely > for the use of the individual or entity named on this message. If you are > not the intended recipient, and have received this message in error, > please notify us immediately by reply e-mail and then delete it from > your system. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
