awk to change value of field using multiple conditions
In the below awk in the first step I default Classification NF-1 to VUS. Next, I am trying to change the value of Classification (NF) to whatever CLINSIG (NF-1) is. If there is only one condition everything works great, but if there are two conditions it does not work. Is the syntax used incorrect or how do I fix the awk? Thank you .
input
Code:
Chr Start End Ref Alt Func.refGene PopFreqMax CLINSIG Classification
chr1 43395635 43395635 C T exonic 0.12 Benign VUS
chr1 43396414 43396414 G A exonic 0.14 Benign VUS
chr1 172410967 172410967 G A exonic 0.66 VUS
chr1 172411496 172411496 A G exonic 1 VUS
chr2 51254901 51254901 G A exonic 0.48 Likely Benign VUS
chr2 51254914 51254914 C T exonic 0.0023 VUS
awk for step 1
Code:
awk 'BEGIN{OFS="\t"} NR>1{$(NF+1)="VUS"} 1' input > out
awk for step 2
Code:
awk -v OFS='\t' '$(NF-1)=="Benign" || $(NF-1)=="Likely Benign" {$(NF)=$(NF-1)} {print $0 }' out > final
desired output
Code:
Chr Start End Ref Alt Func.refGene PopFreqMax CLINSIG Classification
chr1 43395635 43395635 C T exonic 0.12 Benign VUS Benign
chr1 43396414 43396414 G A exonic 0.14 Benign VUS Benign
chr1 172410967 172410967 G A exonic 0.66 VUS
chr1 172411496 172411496 A G exonic 1 VUS
chr2 51254901 51254901 G A exonic 0.48 Likely Benign VUS Likely Benign
chr2 51254914 51254914 C T exonic 0.0023 VUS
Last edited by cmccabe; 08-02-2016 at 02:50 PM..
Reason: add desired output
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08-02-2016
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