
                                 acdtrace 



Function

   Trace processing of an application ACD file (for testing)

Description

   acdtrace reads and processes an ACD file, prompting the user as
   necessary in exactly the same way as if the application itself was
   running. If it encounters an error it will terminate. This allows the
   behaviour of the command-line interface to be tested under different
   conditions, even if the application itself has not yet been written.

   acdtrace works the same as acdc but reports on the processing of lines
   in an ACD file. It also also prints the results of evaluating any
   variables and operations in the 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

   acdtrace does not have its own options, but takes a single parameter
   which is the name of the EMBOSS application that is being testsed. It
   is invoked by specifying the name of the application to be tested
   along with any command-line options after the name of the utility
   application itself:

   acdtrace ApplicationName Options

   acdtrace will run the command line interface of any EMBOSS program by
   reading its ACD file and processing the command line and user
   responses in exactly the same way as if the true program itself were
   running. The application proper is not run; it is only the ACD file
   that is read. Any command-line options for the application being
   called can be specified. The user is prompted for any required
   parameter values not given on the command line and any input files are
   read. Output files can be specified in any available format however
   they will be empty (the application code is not called so there will
   be no output).

   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 (see
   EMBOSS Users Manual for further information).

References

Warnings

   The output on screen can look a little confusing but is by far the
   best way to see how variables and operations work in your ACD file.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name Description
   acdc Test an application ACD file
   acdpretty Correctly reformat an application ACD file
   acdtable Generate an HTML table of parameters from an application ACD
   file
   acdvalid Validate an application ACD file

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
