Is the query itself a significant amount of work for the MySQL server, or is it merely a repeated query for 1M SNPs and thus 1M calls to the server ? How much time does a single query take ? What would be the approximate total time for all the queries ?
A significant hit to the MySQL server means that it isn't so overloaded that it can't do anything else. See if you can work it so it doesn't lock up entirely and lock out other users. If it can still function while you run your queries, that would be acceptable. As a work-around, you could load the tables of interest into a local MySQL server of your own and perform the queries locally. --Hiram Hani Neuvirth-Telem wrote: > Dear Hiram, > > Thanks, but these two option will not work for me: > 1) I need an automatic way to perform the query > 2) I need a join of the SNPs table with some other annotations tables. > > Is there any alternative? > Thanks, > Hani > > -------------------------------------- > Hani Neuvirth-Telem > Machine Learning and Data Mining Group > IBM Research Lab, Israel > Phone: 972-3-7689-404 > E-mail: [email protected] > > > > From: > Hiram Clawson <[email protected]> > To: > Hani Neuvirth-Telem/Haifa/i...@ibmil > Cc: > [email protected], Ariel Farkash/Haifa/i...@ibmil > Date: > 23/12/2009 23:56 > Subject: > Re: [Genome] extracting data for ~1M SNPs > > > > Good Afternoon Hani: > > You may be able to do your query with the table browser: > http://genome.ucsc.edu/cgi-bin/hgTables?db=hg18 > > Select: group "Variation and Repeats" track: SNPs (130) > > Or perhaps download the actual SNP file: > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/snp130.txt.gz > > and fetch your information from that file. > > --Hiram > > Hani Neuvirth-Telem wrote: >> Hello, >> >> We would like to downloading from the UCSC database some data for ~1M >> SNPs. >> In your web site you ask not to perform heavy queries through the MySQL >> server. >> What is the recommended way to perform such queries? >> (Web-sevice/JDBC)? >> >> Thank you, >> Hani > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
