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acdtrace.html
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<HTML>
<HEAD>
<TITLE>
EMBOSS: acdtrace
</TITLE>
</HEAD>
<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="emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
acdtrace
</font></b>
</td></tr>
</table>
<br>
<p>
<H2>
Function
</H2>
ACD compiler on-screen trace
<H2>
Description
</H2>
Acdtrace reports the processing of lines in an ACD file, including the
resolution of any variables or ACD functions.
<p>
Acdtrace does not have its own command line. Instead, it will run the
command line of any EMBOSS program by reading its ACD file and
processing the command line and user responses in exactly the same way
as the true program.
<p>
Acdtrace uses a very simple method. The first command line parameter is
the name of the EMBOSS program to be compiled. All other command line
parameters and qualifiers are processed by that program's ACD file.
<H2>
Usage
</H2>
<b>Here is a sample session with acdtrace</b>
<p>
<p>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% <b>acdtrace antigenic </b>
Finds antigenic sites in proteins
Input protein sequence(s): <b>tsw:actb1_fugru</b>
Minimum length of antigenic region [6]: <b></b>
Output report [actb1_fugru.antigenic]: <b></b>
</pre></td></tr></table><p>
<p>
<a href="#input.1">Go to the input files for this example</a><br><a href="#output.1">Go to the output files for this example</a><p><p>
<H2>
Command line arguments
</H2>
The first parameter is the name of the program to compile.
All other command line parameters and qualifiers are defined for that
program - see the documentation for the program of choice.
<P>
<H2>
Output file format
</H2>
<p>
The output file is empty, but any format available to the specified
program can be used.
<p>
<a name="output.1"></a>
<h3>Output files for usage example </h3>
<p><h3>File: actb1_fugru.antigenic</h3>
<table width="90%"><tr><td bgcolor="#CCFFCC">
<pre>
</pre>
</td></tr></table><p>
<H2>
Data files
</H2>
Acdtrace will use any data files specified in the ACD file of the
specified program, but will ignore any data files that are only used
directly by the program's code.
<p>
EMBOSS data files are distributed with the application and stored
in the standard EMBOSS data directory, which is defined
by the EMBOSS environment variable EMBOSS_DATA.
<p>
To see the available EMBOSS data files, run:
<p>
<pre>
% embossdata -showall
</pre>
<p>
To fetch one of the data files (for example 'Exxx.dat') into your
current directory for you to inspect or modify, run:
<pre>
% embossdata -fetch -file Exxx.dat
</pre>
<p>
Users can provide their own data files in their own directories.
Project specific files can be put in the current directory, or for
tidier directory listings in a subdirectory called
".embossdata". Files for all EMBOSS runs can be put in the user's home
directory, or again in a subdirectory called ".embossdata".
<p>
The directories are searched in the following order:
<ul>
<li> . (your current directory)
<li> .embossdata (under your current directory)
<li> ~/ (your home directory)
<li> ~/.embossdata
</ul>
<p>
<H2>
Notes
</H2>
<H2>
References
</H2>
<H2>
Warnings
</H2>
None.
<H2>
Diagnostic Error Messages
</H2>
<H2>
Exit status
</H2>
It exits with status 0.
<H2>
Known bugs
</H2>
None.
<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="acdc.html">acdc</a></td>
<td>ACD compiler</td>
</tr>
<tr>
<td><a href="acdpretty.html">acdpretty</a></td>
<td>ACD pretty printing utility</td>
</tr>
<tr>
<td><a href="acdtable.html">acdtable</a></td>
<td>Creates an HTML table from an ACD file</td>
</tr>
<tr>
<td><a href="acdvalid.html">acdvalid</a></td>
<td>ACD file validation</td>
</tr>
</table>
<H2>
Author(s)
</H2>
Peter Rice (pmr © ebi.ac.uk)
<br>
Informatics Division, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
<H2>
History
</H2>
<H2>
Target users
</H2>
This program is intended to be used by developers of applications and
interfaces.
<H2>
Comments
</H2>
None
</BODY>
</HTML>