If all of your header names are exactly two alphabetic characters followed by one or more numeric characters, you could change the sort command for the column headings from:

Code:

sc="sort -o " tmpfile

to:

Code:

csc="sort -k1.1,1.2 -k1.3n,1 -o " tmpfile

and use csc (column sort command) instead of sc when sorting the column headers. But if only some of your names fit this pattern, the easiest thing to do is to rename your headers so they have leading zeros to make an alphabetic sort work, (i.e., SA01, SA02, SA03, SA05, SA10, SA11, SA15, SA25, and SA27). This could be coded into the awk program, but I don't have the time to devote to adding the leading zeros before sorting them, stripping off the leading zeros after sorting them, and figuring out what to do if one of you input column names already as a 0 followed by other numeric characters.

Do you also have a problem with sort order for the first field in the rows in your matrix?