Hello Simon, The Jaspar people altered the structure and content of their ftp server recently. There is a patch in the fixes/patches area of the EMBOSS ftp server which updates jaspextract and jaspscan appropriately. The README.fixes file in the 'fixes' directory explains further.
HTH Alan > I've been trying to use EMBOSS to search using the Jaspar database > (jaspextract / jaspscan), but with no success. > > I think the problem is coming from jaspextract. TFM says: > > Input file format > > The input files are the uncompressed and extracted JASPAR_CORE.tgz, > JASPAR_FAM.tgz and JASPAR_PHYLOFACTS.tgz files provided in the > JASPAR > MatrixDir download directory of the JASPAR homepage > (http://jaspar.genereg.net). > > > ..but there are no files named that way (the only google hit to those > names is the jaspextract manpage!). > > The main jaspar archive file is Archive.zip. If I unzip this and run > jaspextract on the expanded directory it runs with no errors or > warnings, but if I subsequently try to run jaspscan I get an error > saying: > > Warning: Matrix file(s) *.pfm not found > > EMBOSS An error in jaspscan.c at line 870: > Matrix list file JASPAR_CORE/matrix_list.txt not found > > I've tried loads of different subdirectories within the JASPAR > database dump, but can't find anything which actually puts data into > the appropriate EMBOSS data directories. > > Can anyone else make this work? > > Thanks > > Simon. > _______________________________________________ > EMBOSS mailing list > EMBOSS@lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/emboss > _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss
