Hello, There are a few options for batch queries:
1) Use the Table browser. There are many functions: create custom tracks, merge data with other tables, intersections, etc. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser 2) Use the public mySQL sever and write your own queries. http://genome.ucsc.edu/FAQ/FAQdownloads#download29 3) Use the flat files and use our utilities or create your own. http://genome.ucsc.edu/FAQ/FAQdownloads#download1 (see download27 below for source code) http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities 4) Create your own mirror of the browser, with just the data you wish to access. http://genome.ucsc.edu/FAQ/FAQlicense http://genome.ucsc.edu/FAQ/FAQdownloads#download27 http://genomewiki.ucsc.edu/index.php/Mirror Large batch (program driven) queries against the main web browser is not allowed. Smaller queries may be succesful but are not encouraged. The timing has to be slow enough or your jobs will become slower and slower and eventually blocked. A block will decay, but this also takes time. Instead, do one of the four above. http://genome.ucsc.edu/FAQ/FAQdownloads#download32 http://genome.ucsc.edu/FAQ/FAQdownloads#download2 Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Jeremy Shearman" <[email protected]> wrote: > From: "Jeremy Shearman" <[email protected]> > To: [email protected] > Sent: Wednesday, November 4, 2009 4:26:36 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] large batch queries > > Hi > I would like to inquire about more efficient ways to do large batch > queries. > I got the message below after submitting several batches and may need > to do more > still. > > Sincerely > Jeremy > > > "There is a very high volume of traffic coming from your site (IP > address > 149.171.177.77) as of Wed Nov 4 04:18:40 2009 (California time). So > that other > users get a fair share of our bandwidth, we are putting in a delay of > 10.0 > seconds before we service your request. This delay will slowly > decrease over a > half hour as activity returns to normal. This high volume of traffic > is likely > due to program-driven rather than interactive access, or the > submission of > queries on a large number of sequences. If you are making large batch > queries, > please write to our [email protected] public mailing list and > inquire about > more efficient ways to access our data. If you are sharing an IP > address with > someone who is submitting large batch queries, we apologize for the > inconvenience. Please contact [email protected] if you think > this delay is > being imposed unfairly." > ------------------------------------------------------------------------------- > Jeremy Shearman, PhD Student. > School of Biotechnology and Biomolecular Sciences > University of New South Wales > Sydney, Australia 2052 > > ph +61 (02) 9385 3840 > fax +61 (02) 9385 1483 > > You live and learn. At any rate, you live. > - Douglas Adams > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
