acdc



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Function

   Test an application ACD file

Description

   acdc 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.

Usage

   Here is a sample session with acdc


% acdc 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

   Acdc 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

   acdc 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:

   acdc ApplicationName Options

   acdc is the basic tool for testing an ACD file works correctly and is
   the most widely used of the utility applications. It 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 values for required
   parameters 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).

   acdc 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 the
   EMBOSS Users Manual for further information).

References

Warnings

   None.

Diagnostic Error Messages

Exit status

   It exits with status 0.

Known bugs

   None.

See also

   Program name     Description
   acdpretty        Correctly reformat an application ACD file
   acdtable         Generate an HTML table of parameters from an application ACD
                    file
   acdtrace         Trace processing of an application ACD file (for testing)
   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

   Completed 9th March 1999

Target users

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

Comments

   None