[EMBOSS] Data for Jasextract

[ajb at ebi.ac.uk]

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.
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