Here's a command-line version (see perlrun) (update: this code processes line-by-line, so it should work on any file — unless a "line" is more than a couple GB long! :). Caution: This only works with Perl versions 5.10+ because it uses the \K regex operator (see Extended Patterns). If you have a pre-5.10 Perl version, let me know; a simple fix can be had (update: what the heck; the pre-5.10 substitution is s{ ^ (> \d+) \n }{$1\t}xms with all else the same).
c:\@Work\Perl\monks\yueli711>type 1.fa
>1
AGTCGTAGCAT
>2
TGAGCTACG
>3
GGCATAGN
>4
CGCACNCAGCTACACC
>5
NGATAGCTACA
c:\@Work\Perl\monks\yueli711>perl -pe "s{ ^ > \d+ \K \n }{\t}xms" 1.f
+a > 1.txt
c:\@Work\Perl\monks\yueli711>type 1.txt
>1 AGTCGTAGCAT
>2 TGAGCTACG
>3 GGCATAGN
>4 CGCACNCAGCTACACC
>5 NGATAGCTACA
This runs under Windows. I can't test this, but I think if you're running under *nix, just replace all the
" (double-quotes) in the command-line with
' (single-quotes).
Give a man a fish: <%-{-{-{-<