acdvalid

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Function

Description

acdvalid processes an ACD file and reports any errors or warnings caused by incorrect, deprecated or obsolete syntax. The tests go above and beyond those of acdc and acdtrace. It highlights ACD syntax that might cause problems to third-party parsing software which wrap the EMBOSS applications.

acdvalid validates the ACD file, testing many features which will not prevent an application from running, but will create problems for the interfaces, whether on the command-line or some other type.

Usage

% acdvalid antigenic 

Command line arguments

Validate an application ACD file
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers: (none)
   Advanced (Unprompted) qualifiers: (none)
   Associated qualifiers: (none)
   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

Output file format

The output file is empty, but any format available to the specified program can be used.

Data files

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

acdvalid 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:

acdvalid ApplicationName Options

acdvalid 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 application parameters 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).

acdvalid 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).

acdvalid generates both error and warning messages. If the message is an "Error" then the ACD file will not work and requires fixing. Most of the messages from acdvalid are "Warnings" and do not prevent a program from running, however it is still worth trying to fix the problem.

Although the warning messages are only advisory, as many warnings as possible are fixed for any application in the main release. Further validation tests will be added in future releases so it is worth running acdvalid on all local ACD files with each new version of EMBOSS

References

Warnings

Diagnostic Error Messages

Exit status

Known bugs

See also

Author(s)

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

History

Target users

Comments