Notes on how to convert from pima.sh output to pretty format.

        Converting pima.sh output file to format for GCG prettyplot
                program (To create publication quality boxed alignment.)



Here are some instructions on how to convert your mase output file from
pima to a pretty text file and a prettyplot postscript file.
You can run these programs on mbcrr and cyrus.

cyrus% mkdir gcgtest
cyrus% cp inter4-SB.mase gcgtest
cyrus% cd gcgtest
~/medtest/inter4/gcgtest

(Now, change "-" to "." in the mase file because the gcg programs use
	a "." for a gap character instead of a "-". )
	% sed 's/-/./g' inter-SB.mase > new.mase

cyrus% 
cyrus% fromig new.mase			***Converts IG files to gcg format
fromig: Command not found.		*** you must be in gcg to use this
cyrus% gcg
cyrus% fromig new.mase

cyrus% dir
total 11
   1 1bbn3.                1 il4_pig.              1 inter4-sb23.
   1 1itl23.               2 inter4-SB.mase        1 inter4-sb3.
   1 1rcb123.              1 inter4-sb.
   1 il4_human123.         1 inter4-sb123.
cyrus% delete inter4-sb*		**** To delete all files that begin
					     with the pattern name inter4-sb
cyrus% delete new.mase			**** Only sequence files in directory.
cyrus% pretty -con -case *		**** To create text file pretty.pretty
					**** The boxed file is created with
					     the prettyplot command below.

Your text output file will be saved in the file pretty.pretty

Note:  As of September 1997, the egcg package is still not available, so the
following commands will not work.

cyrus% egcg
               extensions to GCG (EGCG)  initialized.

					**** In the command below,  "*." refers
					     to all files that end with a "."
					     which is all the gcg files.
cyrus% prettyplot -con -case -shortname *.

Your boxed output file will be sent to the default system printer.
(On cyrus this is the 	qms  printer.)