Unfortunately, as of this time it wants to connect to the database via hdb.h to get chrom sizes with hChromSize which functions by doing this: "select * from chromInfo where chrom = '%s'"
I guess you could make a database with just the chromInfo table for your assembly. Otherwise, somebody has to do some coding to get around this limitation. We also have a few other utilities that have the same simple dependency on the db for chromInfo sizes. Even if we had written the code for an option to read chrom sizes from a file, the makefile sort of has the reference to the mysql stuff hardwired. This would also take some effort for automatic handling. Maybe someday we will be able to do a better job of separating out mysql dependencies from our code base. Sorry for the inconvenience. -Galt On Thu, 27 Aug 2009, Khrebtukova, Irina wrote: > Does genePredToFakePsl work with database only? Do I have to have a > genome database to use the program even if I have already genePred file? > > > > Thanks! > > > > Irina Khrebtukova, PhD > > Sr. Staff Bioinformatics Scientist > > Gene Expression Applications R&D > > > > Illumina Inc. > > 25861 Industrial Blvd., > > Hayward, CA 94545 > > ph: 510-723-9219 > > [email protected] > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
