arithmetic operations on 1 column of a file

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# 1  
Old 12-10-2010
arithmetic operations on 1 column of a file


I have a file with thousands of lines like this:
Chr1    477515    .    ACCCC    ACCC    17.7    .    INDEL;DP=17;AF1=1;CI95=0.5,1;DP4=0,1,0,3;MQ=32;PV4=1,0.036,1,1
Chr1    481987    .    A    AAAT    62    .    INDEL;DP=11;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=41

I want to make a file with the sum of the first 2 numbers after DP4 in one column and the sum of the last two numbers of DP4 (before ;MQ...) in another column. How can I do that simply with some unix commands?

Expected output (for the two example lines above):
1 3
0 4

Last edited by Scott; 12-10-2010 at 01:05 PM.. Reason: Please use code tags
# 2  
Old 12-10-2010
To keep ip simple, I'd use sed to strip it and awk to sum it:
$ sed "s/.*DP4=//;s/;.*//" file1 | awk -F, '{print $1+$2,$3+$4}'
1 3
0 4

# 3  
Old 12-10-2010
And to make it a bit more complex Smilie
awk -F'[=,]' '$1=="DP4"{print $2+$3,$4+$5}' RS=\; file

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