|Think about Loose Coupling|
Re: Lower-casing Substrings and Iterating Two Files togetherby BrowserUk (Pope)
|on Dec 27, 2008 at 14:31 UTC||Need Help??|
If you bitwise or (|) an uppercase letter with a space, (assuming latin-1/ASCII files), it will lowercase it:
So, if you translate all the 'N's in your mask to spaces and then bitwise or the sequence and the mask, it will achieve your goal very efficiently:
Which makes your entire program (excluding the unmentioned fact that your files may be in FASTA format):
Redirect the output to a third file and you're done.
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