Sorry-- I'm not sure where the hgWiggle program is. I have the CVS repository but I don't see it under src/hg I only see wiki pages describing downloading the repo, not building or using specific tools. Where is the manual for all this stuff?
-- Jake Biesinger On Mon, Aug 31, 2009 at 8:07 AM, Jacob Biesinger <[email protected]>wrote: > > > Begin forwarded message: > > *From: *Hiram Clawson <[email protected]> > *Date: *August 30, 2009 8:27:01 PM PDT > *To: *Jacob Biesinger <[email protected]> > *Cc: *[email protected] > *Subject: **Re: [Genome] PhastCons scores programmatically?* > > Good Evening Jacob: > > The kent source tree command: hgWiggle can be used to > fetch regions from these files. See also: > > http://genomewiki.ucsc.edu/index.php/Using_hgWiggle_without_a_database > > The actual original scores can be found in the files: > ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ > > but there is no real access method to those file, they are simple > ASCII files which you would have to read and parse in order to > get the scores out of them. You might be able to convert them > to bigWig files and use the access program for those files. > See also: > ftp://hgdownload.cse.ucsc.edu/apache/htdocs/admin/exe/linux.x86_64/ > > --Hiram > > Jacob Biesinger wrote: > > Hi! > > Interested in getting the PhastCons score for a few thousand regions in > Drosophila melanogaster. I could use galaxy, but I'd rather have > programmatic access to the data (there's no command line interface in > Galaxy, unfortunately!) > > The public mysql server is set up to only give me the offsets in the > appropriate phastCons score files. Is there any way to get those scores > programmatically short of pulling those files down, getting the offset etc > etc? > > Thanks! > > -- > > Jake Biesinger > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
