Your file 1 has only one line. Is this going to be the case with your real data? If yes, you only need to pick up the lines of file 2 where column two falls between the range defined by file 1.

But if file 1 has several lines, then you need to explain how to do the match between the two files.

From looking at your data, maybe you want this: for each line in file 1, check the ID (e.g. chr11) in the second field, pick up the pivot value in the 4th field (650), and grab in file 2 all lines whose ID is chr11 and whose second field is within the range (650-500..650+500).

If this is what you want, I suggest that you should read the full file 1 and store ID/4th field of each line in a hash. Close File 1. Read file 2, for each line in file 2, check the ID, lookup the pivot value for this ID in the hash, and check if field 2 falls within the range.

In reply to Re: Sliding window perl program by Laurent_R
in thread Sliding window perl program by genome

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