prosextract



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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

Processes the PROSITE motif database for use by patmatmotifs
Version: EMBOSS:6.4.0.0

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

   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers:

   "-prositedir" associated qualifiers
   -extension1         string     Default file extension

   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 and exit. 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
   -version            boolean    Report version number and exit


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 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 formerly at:
   HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

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