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awk if one field has more characters than another

 
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# 1  
Old 08-08-2012
awk if one field has more characters than another
Hi all, I've been stuck on how to write a command in awk that looks at two columns and only prints entries where one of the columns has more than or less than a 3 character difference. I need to be able to compare any two columns preferably, but as an example, comparing columns 3 and 4

example input
Code:
1    2    3    4        5
b    c    AA   G        d
b    c    AA   GGG      d
b    c    AA   GGGGGG   d
b    c    AAAA G        d
b    c    A    G        d

desired output
Code:
b    c    AA   GGGGGG   d
b    c    AAAA G        d

Appreciate the help!!!
# 2  
Old 08-08-2012
Code:
$ awk '{for(i=1;i<=NF;i++)if(length($i)>3){print;next}}' input.txt
b    c    AA   GGGGGG   d
b    c    AAAA G        d

# 3  
Old 08-08-2012
Thanks so much. Question: Is the code comparing field 3 and 4? I think this will look at more than just 3 and 4?? I need to be able to only compare two columns at a time, as there will be over 50 columns with full text.
Thanks
# 4  
Old 08-08-2012
try this for ( 3rd and 4th column )

Code:
$ awk 'length($3)>3 || length($4)>3' input.txt
b    c    AA   GGGGGG   d
b    c    AAAA G        d

my first post was to check whether any of the field length is greater than 3
# 5  
Old 08-08-2012
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.
# 6  
Old 08-08-2012
awk
Hi,

Try this one,
Code:
awk '{l=length($3)-length($4);if(l>=3||l<=-3){print;}}' file

Cheers,
Ranga:-)
Last edited by rangarasan; 08-08-2012 at 02:08 PM..
# 7  
Old 08-08-2012
Thanks for your reply, I will try the code.
Not sure I want the largest with respect to one column, just the ones where there is a magnitude difference of 3.

example
Code:
col3   col4
A      AA       # difference of 1
AAA    A        # difference of 2
A      AAAAA    # difference of 4 PRINT
AAAA   A        # difference of 3 PRINT

And it has to ignore other columns
Thanks!
 
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