in reply to Faulty Control Structures?

but the program doesn't end

Do you mean the program doesn't stop even when you hit return in response to " What is the name of the ChIPOTle file\?"?

Do you mean the program never finds the end of the file it's processing?

My code "works" to some degree, in that it gives me an output

Under what circumstance does it work? For the first file only? For more than one file?

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Re^2: Faulty Control Structures?
by bioinformatics (Friar) on Jan 28, 2008 at 20:43 UTC
    Good questions. The program works on small files, i.e. smaller annotation files of just a few lines that I used to test. They are the same format as the full files. When using the full files however, the program would not exit, even after I started it just prior to leaving on Friday, to come back to it early this morning (didn't think it would take that long :p). I did get information printed in the output file however. The program can find the end of the files, and is designed to annotate just one file at a time.
    Bioinformatics