Why not just make biologists learn UNIX?
Yes, many of these tools can be implemented with UNIX tools like grep, cut, paste, join, awk, sed…. However: UNIX tools tend to give “concise” feedback; they tend to have many, many options; and shell scripting can be even more cryptic than Perl. It’s possible to imagine a Scriptome with cut-and-paste pure UNIX commands instead of Perl, which would get around some of these problems. But using Perl means we can also write biology-specific tools pretty easily (possibly stealing them from Bioperl).
