jaspextract
    Function
    Description
   JASPAR is a collection of transcription factor DNA-binding preferences,
   modelled as matrices. These can be converted into Position Weight
   Matrices (PWMs or PSSMs), used for scanning genomic sequences.
   JASPAR is the only database with this scope where the data can be used
   with no restrictions (open-source).
   This program copies the JASPAR distribution into its component
   matrix sets (e.g. JASPAR_CORE, JASPAR_PHYLOFACTS etc) and copies
   them into the EMBOSS data directories, performing any necessary
   conversions
   The home page of JASPAR
   is: http://jaspar.genereg.net/
   The EMBOSS program jaspscan will not work unless this program is run.
   Running this program may be the job of your system manager.
    Usage
    Command line arguments
    Input file format
The input files are part of the uncompressed and extracted Archive.zip
file provided in the JASPAR html/DOWNLOAD directory of the JASPAR
homepage (http://jaspar.genereg.net).
After extracting the file you should specify the all_data/FlatFileDir
directory when running jasparextract. It is advisable to first delete
any old data files from your EMBOSS data file area e.g. from the
/usr/local/emboss/share/EMBOSS/data/JASPAR_* directories
    Output file format
The output file format is currently the same as the JASPAR
distribution format, but with the matrix files separated into
directories according to their type.
    Data files
None
    Notes
The home page of JASPAR
is: http://jaspar.genereg.net
Running this program may be the job of your system manager.
    References
- DNA binding sites: representation and discovery Bioinformatics. 2000
      Jan;16(1):16-23
- Applied bioinformatics for the identification of regulatory elements
      Nat Rev Genet. 2004 Apr;5(4):276-87 
    Warnings
None.
    Diagnostic Error Messages
None.
    Exit status
It always exits with status 0 unless an error is reported
    Known bugs
None.
    Author(s)
    History
    Target users
    Comments