awk to change value in field according to another Post: 303025742

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Top Forums Shell Programming and Scripting awk to change value in field according to another Post 303025742 by Don Cragun on Sunday 11th of November 2018 06:40:48 AM

11-11-2018

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I'm sorry. I appreciate the lessons I'm getting in genomics, but I still don't understand your requirements.

From your description and examples, I'm guessing that even though you haven't said so:

there will be no overlap in $2-$3 value ranges for any two lines in file2,
all of the lines in file2 that are associated with a $4 value in file1 are adjacent,
the strings in $4 in file1 and at the start of $4 in file2 are irrelevant to this problem (only the ranges specified by $2-$3 matter other than copying the $4 value in file1 into the output),
if a $2 value in file1 is inside one of the $2-$3 ranges in file2, then a new 5th field added to file1 should be set to exon in the output (this comes from the examples, but conflicts with several statements in the English requirements),
if a $2 value in file1 is not inside any $2-$3 range in file2 and the difference $2 on some line in file2 minus $2 on a line in file1 is greater than zero and less than eleven, then a 5th field added to file1 should be set to splicing in the output (this also comes from the examples, but conflicts with the stated English requirements), and
otherwise, a 5th field added to file1 should be set to intron.

Please confirm whether or not my guesses are correct. And, if my guesses are not correct, please restate your requirements and give us an example where the stated requirements and the given examples are consistent with each other.

Note that if file2 is sorted on increasing values of field 2 (as in your example) and file1 was sorted on increasing values of field 2, neither file would have to be loaded into memory and both files could be read one line at a time. (This would make the code more complex, but would reduce the amount of memory needed to run your program if that is an issue.) But, in your sample data, file1 is not sorted.

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