
                                 acdtrace 



Function

   ACD compiler on-screen trace

Description

   Acdtrace reports the processing of lines in an ACD file, including the
   resolution of any variables or ACD functions.

   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.

   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.

Usage

   Here is a sample session with acdtrace


% acdtrace antigenic 
Finds antigenic sites in proteins
Input protein sequence(s): tsw:actb1_fugru
Minimum length of antigenic region [6]: 
Output report [actb1_fugru.antigenic]: 

   Go to the input files for this example
   Go to the output files for this example

Command line arguments

   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.

Output file format

   The output file is empty, but any format available to the specified
   program can be used.

  Output files for usage example

  File: actb1_fugru.antigenic

Data files

   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.

   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.

   To see the available EMBOSS data files, run:

% embossdata -showall

   To fetch one of the data files (for example 'Exxx.dat') into your
   current directory for you to inspect or modify, run:

% embossdata -fetch -file Exxx.dat

   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".

   The directories are searched in the following order:
     * . (your current directory)
     * .embossdata (under your current directory)
     * ~/ (your home directory)
     * ~/.embossdata

Notes

References

Warnings

   None.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name              Description
   acdc         ACD compiler
   acdpretty    ACD pretty printing utility
   acdtable     Creates an HTML table from an ACD file
   acdvalid     ACD file validation

Author(s)

   Peter Rice (pmr © ebi.ac.uk)
   Informatics Division, European Bioinformatics Institute, Wellcome
   Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK

History

Target users

   This program is intended to be used by developers of applications and
   interfaces.

Comments

   None
