Hi dietmar,
If any names are more than 7 characters long (assuming tab stops set at every 8 column positions), your output headings won't line up with the data values. If this is a concern to you, you could change the script to print the top headings vertically instead of horizontally and adjust the printing of the row headings to make the 1st column in your output be the width of the longest name.

Furthermore, with millions of rows and columns, the output produced will not be a text file (due to excessive line lengths), so you will be restricted by the number of utilities you can use to post-process your output.
RudiC has already commented on the part removed above.
Assuming that there are no empty or blank lines in your input files, that column and row headings are less than 8 characters long (or you don't care about column alignment), and that you don't want the extra tab at the end of each line that your script currently produces, you could also try this slightly simplified script:

Code:

#!/bin/bash
fn=$1
fname=${fn%.*}
echo $fname

awk '{  HD[$1]; HD[$3]; PP[$1,$3] = PP[$3,$1] = 1}
END {   for (i in HD) printf "\t%s", i
        printf "\n"
        for (i in HD) {
                printf "%s", i
                for (j in HD) printf "\t%d", PP[i,j]?1:0
                printf "\n"
        }
}' $fn > $fname.adj

which puts:

Code:

	A	B	C	D	E
A	0	1	1	0	0
B	1	0	0	1	0
C	1	0	0	0	0
D	0	1	0	0	1
E	0	0	0	1	0

in your output file when the file named by $1 contains the input given in the 1st message in this thread. (Again as RudiC stated, the order of rows and columns may vary, but the row headings and the column headings should be in the same order.)

If you wanted to run this on a Solaris/SunOS system, you would need to use /usr/xpg4/bin/awk or nawk instead of awk.