CSC

acdtrace

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Function

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

% 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

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

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

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