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I have a list of files where I need to remove some lines that have been added yesterday by a spambot. The section I want to remove looks like this:

^M
<script>[...] bunch of malware code [...]</script>

That section seems to have been appended to the files, so I can be relatively sure it's the last lines of each file that contain this part.

Now I know a bit of Linux, but not enough to do this via a command. How would I go about and do this?

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Is the malware code consistent? does it start and end with the same text in all cases??

If you can write a regexp, you can do something like:

perl -npi.bak -e 's/startofcode.*?endofcode//' file1 file2 file3 orglob*
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or sed if perl is not available on the machine (unusual but could happen) – Ophidian May 14 '10 at 15:33
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