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$ cat inputfile | tr -d '\n' | sed 's/\([^~]*~[^~]*~[^~]*~[^~]*~[^~]*~\)/\1\n/g'
"aa"~"bb"~"001"~""~""~
"cc""dd"~"005"~""~""~"kk"~
"aa"~"008"~""~""~

@mnmonu: You wanted 5 numbers of '~' on a line, right? Sample output is contradicting with your requirement.

$ perl -pe 's/\n//g' inputfile | perl -pe 's/(.+?~.+?~.+?~.+?~.+?~)/$1\n/g'...