awk to add plus or minus to fields and split another field

Shell Programming and Scripting
1

In the tab-delimited input below I am trying to use awk to -10 from $2 and +10 to $3 . Something like

awk -F'\t' -v OFS='\t' -v s=10 '{split($4,a,":"); print $1,$2-s,$3+s,a[2],$5,$6} | awk {split(a[2],b,"-"); print $1,$2-s,$3+s,b[1]-s,b[2]+s,$5,$6}' input

should do that. I also need to -10 from $4 after the : but before the - and +10 from $4 after the : but after the - . Thank you :).

input

chr1    948836    948966    chr1:948836-948966    .    ISG15
chr1    949353    949929    chr1:949353-949929    .    ISG15
chr1    955492    955763    chr1:955492-955763    .    AGRN
chr1    955492    955763    chr1:955492-955763    .    AGRN
chr1    957570    957852    chr1:957570-957852    .    AGRN

desired output (tab-delimited)

chr1    948826    948976    chr1:948826-948976    .    ISG15
chr1    949343    949939    chr1:949343-949939    .    ISG15
chr1    955482    955773    chr1:955482-955773    .    AGRN
chr1    955482    955773    chr1:955482-955773    .    AGRN
chr1    957560    957862    chr1:957560-957862    .    AGRN

awk

awk -F'\t' -v OFS='\t' -v s=10 '{split($4,a,":"); print $1,$2-s,$3+s,a[2],$5,$6} | awk {split($4,b,"-"); print $1,$2-s,$3+s,b[1]-s,b[2]+s,$5,$6}' input
awk: cmd. line:1: {split($4,a,":"); print $1,$2-s,$3+s,a[2],$5,$6} | awk {split($4,b,"-"); print $1,$2-s,$3+s,b[1]-s,b[2]+s,$5,$6}
awk: cmd. line:1:                                                  ^ syntax error
2

Hello cmccabe,

Could you please try following and let me know if this helps you.

awk '{$2-=10;$3-=10;split($4, A,"[:-]");$4=A[1]":"A[2]-10":"A[3]-10;print}'  FS="\t" OFS="\t"  Input_file

Thanks,
R. Singh

1 Like
3 
awk -F"\t" '{$2-=10;$3+=10;$4=$1":"$2"-"$3}1' OFS="\t" input.txt