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
