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awk if one field has more characters than another

 
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# 8  
Old 08-08-2012
Quote:
Originally Posted by torchij
Oh ok. I think what I need the difference between two columns. To provide some context the A's and G's are biological genetic mutation data. One column is the reference, and the other is a tumor sample. I am trying to extract all entries where there is an insertion OR deletion of at least 3base pairs (A's G's C's or T's).

The best way to do this is to look at the reference and tumor column and ask if there is at least a difference of 3 letters.
hmmm... my head starts hurtin' a bit......
Code:
nawk 'sqrt((length($3)-length($4))^2) >=3' myfile

Last edited by vgersh99; 08-08-2012 at 02:17 PM..
This User Gave Thanks to vgersh99 For This Post:
torchij
# 9  
Old 08-08-2012
I think you're asking for something like:
Code:
awk ' function abs_diff(a,b) { return a > b ? a - b : b - a; } abs_diff(length($3),length($4)) >= 3 {print}' < genome_data

or
Code:
awk ' function abs_diff(a,b) { return a > b ? a - b : b - a; } abs_diff(length($3),length($4)) >= 3 {print $3,$4}' < genome_data

This User Gave Thanks to Don Cragun For This Post:
torchij
# 10  
Old 08-08-2012
Thanks!! That's a clever way.
 
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