Alternative ways of invoking ALSCRIPT

The documentation above describes the interactive mode of running ALSCRIPT. However, it may be more convenient to run the program as a pipe under Unix or MS-DOS. Examples are shown here.

ALSCRIPT is a program for producing pretty versions of multiple sequence aligments. ALSCRIPT will also format single sequences. A full description of the program is given in the file "alscript.doc".

Ways of running alscript:

1. Interactive mode: just type alscript. You will be prompted for a command file name. The command file will define the AMPS blocfile, and name of the file to store the PostScript output - see alscript.doc for details.

2. alscript <command_file> has same effect as 1, But does not prompt for the command file e.g. alscript example1.als

3. alscript -q < <blocfile> > <PostScript> Quick mode - uses default commands, reads alignment from stdin, writes PostScript to stdout. This mode creates a command file called ALPSQ.COM.

   e.g. alscript -q < example1.blc > example1.ps

4. alscript -f <command_file> Similar effect to 2.

5. alscript -f <command_file> -s Silent operation: No messages are written to stderr, unless fatal. Silent operation may be toggled by the silent_mode command in the command file.

6. alscript -f <command_file> -p < <blocfile> > <PostScript> Make alscript work like a pipe - blocfile is read from stdin, postscript is written to stdout. Messages are written to stderr. To supress messages include the -s flag too

   e.g. alscript -f example1.als -p -s < example1.blc > example1.ps

Using alscript as a pipe has the advantage of allowing the blocfile to be created on the fly by the programs msf2blc or clus2blc. For example if we have a GCG .msf file called "pileup.msf" we can run alscript with default shading/fonts and send the results straight to the PostScript printer "lpr" as follows:

msf2blc -q <pileup.msf | alscript -q -s | lpr