acdtrace



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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_takru
Minimum length of antigenic region [6]:
Output report [actb1_takru.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_takru.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
   European Bioinformatics Institute, Wellcome Trust Genome Campus,
   Hinxton, Cambridge CB10 1SD, UK

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

History

Target users

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

Comments

   None