|
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.
| 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