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<HTML>

<HEAD>
  <TITLE>
  EMBOSS: prosextract
  </TITLE>
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<BODY BGCOLOR="#FFFFFF" text="#000000">

<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="/images/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
prosextract
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<H2>
Wiki
</H2>

The master copies of EMBOSS documentation are available
at <a href="http://emboss.open-bio.org/wiki/Appdocs">
http://emboss.open-bio.org/wiki/Appdocs</a>
on the EMBOSS Wiki.

<p>
Please help by correcting and extending the Wiki pages.

<H2>
    Function
</H2>
Process the PROSITE motif database for use by patmatmotifs

<H2>
    Description
</H2>

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

<H2>
    Usage
</H2>
Here is a sample session with <b>prosextract</b>
<p>

<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% <b>prosextract </b>
Process the PROSITE motif database for use by patmatmotifs
PROSITE database directory [.]: <b></b>

</pre></td></tr></table><p>
<p>
<a href="#output.1">Go to the output files for this example</a><p><p>

<p>

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.


<H2>
    Command line arguments
</H2>
<table CELLSPACING=0 CELLPADDING=3 BGCOLOR="#f5f5ff" ><tr><td>
<pre>
Process the PROSITE motif database for use by patmatmotifs
Version: EMBOSS:6.6.0.0

   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

</pre>
</td></tr></table>
<P>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-prositedir]<br>(Parameter 1)</td>
<td>directory</td>
<td>PROSITE database directory</td>
<td>Directory</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Associated qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td align="left" colspan=5>"-prositedir" associated directory qualifiers
</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -extension1<br>-extension_prositedir</td>
<td>string</td>
<td>Default file extension</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>General qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td> -auto</td>
<td>boolean</td>
<td>Turn off prompts</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -stdout</td>
<td>boolean</td>
<td>Write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -filter</td>
<td>boolean</td>
<td>Read first file from standard input, write first file to standard output</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -options</td>
<td>boolean</td>
<td>Prompt for standard and additional values</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -debug</td>
<td>boolean</td>
<td>Write debug output to program.dbg</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -verbose</td>
<td>boolean</td>
<td>Report some/full command line options</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -help</td>
<td>boolean</td>
<td>Report command line options and exit. More information on associated and general qualifiers can be found with -help -verbose</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -warning</td>
<td>boolean</td>
<td>Report warnings</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -error</td>
<td>boolean</td>
<td>Report errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -fatal</td>
<td>boolean</td>
<td>Report fatal errors</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -die</td>
<td>boolean</td>
<td>Report dying program messages</td>
<td>Boolean value Yes/No</td>
<td>Y</td>
</tr>

<tr bgcolor="#FFFFCC">
<td> -version</td>
<td>boolean</td>
<td>Report version number and exit</td>
<td>Boolean value Yes/No</td>
<td>N</td>
</tr>

</table>


<H2>
    Input file format
</H2>


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

<p>


<H2>
    Output file format
</H2>


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)

<p>


<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>Directory: PROSITE</h3>
<p>This directory contains output files.
<p>


<H2>
    Data files
</H2>


See Input file format above.

<H2>
    Notes
</H2>

<p>This program most be run as a prerequisite to using <b>patmatmotifs</b>.</p>

<H2>
    References
</H2>


<ol>
<li>Bairoch, A., Bucher P. (1994) PROSITE: recent developments. Nucleic 
Acids Research, Vol 22, No.17 3583-3589.

<li>Bairoch, A., (1992) PROSITE: a dictionary of sites and patterns in 
proteins. Nucleic Acids Research, Vol 20, Supplement, 2013-2018.

<li>Peek, J., O'Reilly, T., Loukides, M., (1997) Unix Power Tools, 2nd 
Edition.
</ol>

<H2>
    Warnings
</H2>


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

<H2>
    Diagnostic Error Messages
</H2>


As in warnings.

<H2>
    Exit status
</H2>


Always exits with status 0

<H2>
    Known bugs
</H2>


<h2><a name="See also">See also</a></h2>
<table border cellpadding=4 bgcolor="#FFFFF0">
<tr><th>Program name</th>
<th>Description</th></tr>
<tr>
<td><a href="aaindexextract.html">aaindexextract</a></td>
<td>Extract amino acid property data from AAINDEX</td>
</tr>

<tr>
<td><a href="cutgextract.html">cutgextract</a></td>
<td>Extract codon usage tables from CUTG database</td>
</tr>

<tr>
<td><a href="jaspextract.html">jaspextract</a></td>
<td>Extract data from JASPAR</td>
</tr>

<tr>
<td><a href="printsextract.html">printsextract</a></td>
<td>Extract data from PRINTS database for use by pscan</td>
</tr>

<tr>
<td><a href="rebaseextract.html">rebaseextract</a></td>
<td>Process the REBASE database for use by restriction enzyme applications</td>
</tr>

<tr>
<td><a href="tfextract.html">tfextract</a></td>
<td>Process TRANSFAC transcription factor database for use by tfscan</td>
</tr>

</table>


<H2>
    Author(s)
</H2>


Sinead O'Leary formerly at:
<br>
HGMP-RC, Genome Campus, Hinxton, Cambridge CB10 1SB, UK


<p>
Please report all bugs to the EMBOSS bug team (emboss-bug&nbsp;&copy;&nbsp;emboss.open-bio.org) not to the original author.


<H2>
    History
</H2>


Completed March 24 1999.

<H2>
    Target users
</H2>
This program is intended to be used by administrators responsible
for software and database installation and maintenance. 


<H2>
    Comments
</H2>
None


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