Shell Programming and Scripting

There are 146 lines below the header. Sorry its not clear.
The lines from the counts files are created from an other file which contains 6,000,000 lines.
This file contains 6,000,000 sequences of length 146 with numbers 1,2,3, and 4.
I want to count the occurrences of all combinations of 1,2,3 and 4. So for example: 1 in position 1 in all sequences, and 3 in position 5 in all sequences.
So those counts are 146 x 146 matrices with counts of occurrences of all those possible combinations.

-------A=1,B=1-------
occurrences of 1 in one position and 1 in an other position
146x146 matrix

Hope its clear now...

I'm even less sure how. So the input is a 147x147 matrix, or I'm supposed to assemble a 147x147 matrix out of lines?

If you could just show more of your input and output instead of hoping we'll make correct assumptions about stuff you never posted, then show the work you did to generate one from the other, that would help a lot more than describing something we can't see over and over. Shrink the example to something you can show in its entirety, like a 3x3 instead of a 147x147. Ideally the same code could apply to either.

Please start using code tags as indicated before - otherwise you'll loose interesting in this entirely.