what i am looking for is that the script takes the line literally and not apply the new line character
Perhaps it's just me, but I don't understand what you mean there - you want Perl to 'take the line literally'? (rather than taking it figuratively or metaphorically?)
Could you re-phrase this, it's not clear (to me at least) why just taking out the newline characters with tr/// won't give you the result you want.
update: re-reading the original question, it looks like its the concept of 'new line characters in the middle of a line' which is proving slippery. Not to sound pedantic, but I've never seen a newline character in the middle of a line. They tend to be at the end of each line.
Do you mean that some of the newlines are ones you want to keep, and some of them are unwanted?
How do you tell apart the ones you want versus the ones you don't want? Maybe if you were to show us a sample of the file, we'd be able to help you better.
Or is this a UNIX-versus-DOS different-newline-characters issue?
update2: or do you mean that some of the newline characters are (or should be) escaped?