awk split and awk calculation in the same command Post: 302969422

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Top Forums Shell Programming and Scripting awk split and awk calculation in the same command Post 302969422 by cmccabe on Tuesday 22nd of March 2016 01:51:10 PM

03-22-2016

Registered User

awk split and awk calculation in the same command

I am trying to run the awk below. My question is when I split the input, then run anotherawk to perform a calculation using that splitas the input there are no issues. When I try to combine them the output is not correct, is the split not working or did I do it wrong? Thank you Smilie

.

input

Code:

 
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    1    15
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    2    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    3    16
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    4    14
chr1    955543    955763    chr1:955543-955763    AGRN-6|gc=75    5    17

after the split awk '{split($5,a,"-"); print $1,$2,$3,$4,a[1]}' input > split

split (uses the - in $5 and prints $1,$2,$3,$4,and the split a[1]

Code:

chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN

if I use that file (split) in the below awk the output is correct

output ($5 count of lines that are the same and the sum of $3-$2

Code:

AGRN 5 1100

If I try to perform the split and run the calculation in the same awk, I get the below output:

Code:

awk '{split($5,a,"-"); print $1,$2,$3,$4,a[1]} {c1[a1]++; c2[a1]+=($3-$2)}
>     END{for (e in c1) print e, c1[e], c2[e]}' split

output

Code:

chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
chr1 955543 955763 chr1:955543-955763 AGRN
 5 1100

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