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Yeah, what OS. Proprietary won't give you the same leg up as, say, a Unix variant, usually. Check the documentation and see what utilities it gives you in the way of recording files. It may have one already that will copy the serial port to a file. It may have the ability to treat the serial port as a sort of stdin and copy it to a file via redirection. It may have an API that lets you talk to a disk in a relatively simple manner, without worrying about the file system and it's organization. In a case like that, you might only have to read the serial port, buffer it up, and pop it to the disk. If your data acquisition is something that takes significant time, you probably aren't going to want to block the normal operation of the development system. Serial ports usually give you the ability to run off of interrupts. Your OS, if multiprocessing (not a given, depends on the development system), can relieve you of that task.
Read the documentation for your system. The answers might be right there. If not, post back with the kind of system it is, with some details. Or, if it's not a one-off, give the model number or something and we can delve into it a little bit.
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