
                                prosextract 



Function

   Processes the PROSITE motif database for use by patmatmotifs

Description

   prosextract processes the PROSITE motif database for use by
   patmatmotifs. It reads the prosite.dat and prosite.doc files (from the
   Prosite distribution) from the specified directory and writes an
   output file (by default called prosite.lines) with the following
   information (corresponding lines from prosite.dat given in
   parentheses): i. Identity (ID). ii. Accession number (AC). iii. Motif
   pattern (PA). iv. The motif pattern converted a regular expression.
   Additionally, one output file per accession number is written
   containing documentation from prosite.doc.

Usage

   Here is a sample session with prosextract


% prosextract 
Processes the PROSITE motif database for use by patmatmotifs
PROSITE database directory [.]: 

   Go to the output files for this example

   The output files named after the prosite accession numbers can now
   also be seen in the prosite directory. This files are automatically
   created after prosextract is run.

Command line arguments

   Standard (Mandatory) qualifiers:
  [-prositedir]        directory  PROSITE database directory

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages

                 Standard (Mandatory) qualifiers      Allowed values Default
   [-prositedir]
   (Parameter 1) PROSITE database directory Directory
                 Additional (Optional) qualifiers     Allowed values Default
                 (none)
                 Advanced (Unprompted) qualifiers     Allowed values Default
                 (none)

Input file format

   These files must be the "prosite.dat" and "prosite.doc" file of a
   Prosite distribution, containing all current prosite data.

Output file format

   These files are held in the prosite subdirectory of the emboss data
   directory. The default names are "prosite.lines" and "PS*****"
   (accession number documentation files)

  Output files for usage example

  Directory: PROSITE

   This directory contains output files.

Data files

   See Input file format above.

Notes

   This program most be run as a prerequisite to using patmatmotifs.

References

    1. Bairoch, A., Bucher P. (1994) PROSITE: recent developments.
       Nucleic Acids Research, Vol 22, No.17 3583-3589.
    2. Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in
       proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.
    3. Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd
       Edition.

Warnings

   The program will warn the user if the input file is incorrectly
   formatted.

Diagnostic Error Messages

   As in warnings.

Exit status

   Always exits with status 0

Known bugs

See also

   Program name Description
   aaindexextract Extract amino acid property data from AAINDEX
   cutgextract Extract codon usage tables from from CUTG database
   jaspextract Extract data from JASPAR
   printsextract Extract data from PRINTS database for use by pscan
   rebaseextract Process the REBASE database for use by restriction
   enzyme applications
   tfextract Process TRANSFAC transcription factor database for use by
   tfscan

Author(s)

   Sinead O'Leary (current e-mail address unknown)
   while she was at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

History

   Completed March 24 1999.

Target users

   This program is intended to be used by administrators responsible for
   software and database installation and maintenance.

Comments

   None
