... print it out with the string to insert at the end ...

Doesn't that leave you with a  'nnnnnwhatevernnnnn' "joiner" sequence pasted at the end of the last line of the file? My interpretation of the OP was that joiners should be pasted only between the "contig" sequences. (But I have done no testing of your code.)

In reply to Re^2: merge sequences with new sequence insertion by AnomalousMonk
in thread merge sequences with new sequence insertion by utpalmtbi

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