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We recently published (LGPLv3-compatible) FUSTA, a software utility dedicated to the manipulation of FASTA files, especially adding & removing sequences, easily accessing subsequences (wouldn't cat myfasta/get/chr3:10000-12000 be pretty nifty?), altering sequences (think case modification), renaming sequences (gosh, should we use chrX or X?), and accessing individual sequences as independent files (you don't really need to blast all of these 11864 proteins, do you?).
Now, I guess the deeper question is ‶is the text-based, line-delimited, pipe-oriented, interaction model between programs that don't know each other still relevant″; and we have seen new, more structured, approaches being tested, for instance with PowerShell or NuShell.