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acdtrace |
Acdtrace 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.
Acdtrace 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.
% acdtrace antigenic Finds antigenic sites in proteins Input protein sequence(s): tsw:actb1_fugru Minimum length of antigenic region [6]: Output report [actb1_fugru.antigenic]: |
Go to the input files for this example
Go to the output files for this example
The output file is empty, but any format available to the specified program can be used.
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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:
| Program name | Description |
|---|---|
| acdc | ACD compiler |
| acdpretty | ACD pretty printing utility |
| acdtable | Creates an HTML table from an ACD file |
| acdvalid | ACD file validation |