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5. Example scripts

The distribution includes 2 sets of example scripts. A listing of included scripts is given on the WWW site.

(A) The examples directory has a README file and a variety of scripts. For each tool in there is a script that invokes the tool on a simple data set (from the files sub-directory) and exercises various tool methods. These scripts are meant to illustrate how the tool is used.

Assuming is in your path, each of the test scripts can be run from within the examples directory by typing one of these lines (from the shell or from within

% -f
> @run 

The remaining scripts in the examples directory illustrate how to do various tasks in They are not meant to be generically useful nor are they well documented. Rather they are illustrations of how to do some specific task quickly and straightforwardly. Most of these scripts are not meant to be run by other users, since their data files are not included.

(B) The scripts directory contains several scripts you may find useful either to use directly or to modify to create a new script for your purposes.

The top of each script file describes its purpose and syntax. That information can be be accessed from within by typing "??" or "?" or "??".

As explained in this section, any file in the scripts directory can be run from the directory where your data lives, by typing a line appropriate to the script's syntax, e.g.

% -f svg 60 135 dump.protein      from the shell
> @run svg 60 135 dump.protein             from