
                                 antigenic 



Function

   Creates an HTML table from an ACD file

Description

   Acdtable is used to generate the HTML table of command line options
   for an EMBOSS program.

   Acdtable 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.

   Acdtable 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 acdtable


% acdtable antigenic 


 Standard (Mandatory) qualifiers
 Allowed values
 Default



 [-sequence]
(Parameter 1)
 Protein sequence(s) filename and optional format, or reference (input USA)
 Readable sequence(s)
 Required



 -minlen
 Minimum length of antigenic region
 Integer from 1 to 50
 6



 [-outfile]
(Parameter 2)
 Output report file name
 Report output file
 <*>.antigenic



 Additional (Optional) qualifiers
 Allowed values
 Default



 (none)



 Advanced (Unprompted) qualifiers
 Allowed values
 Default



 (none)




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.

Data files

   Acdtable 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
   acdtrace     ACD compiler on-screen trace
   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
