CODEWITHSUNDEEP
linuxjoinawk
a_avelar
a_avelar

Reputation: 33

Replace two columns linux

I want to replace the second column of my first file

file 1:

2       rs58086319      0       983550  T       C
2       rs56809628      0       983571  T       C
2       rs7608441       0       983572  A       G
2       rs114910509     0       983579  A       G
2       var_chr2_983614 0       983614  T       C
2       var_chr2_983624 0       983624  A       G
2       rs115188027     0       983632  A       C
2       var_chr2_983636 0       983636  T       C
2       var_chr2_983650 0       983650  A       G
2       var_chr2_983660 0       983660  T       C

with the first column of my second file

file 2:

2_983550_T_C
2_983571_T_C
2_983572_A_G
2_983579_A_G
2_983614_T_C
2_983624_A_G
2_983632_A_C
2_983636_T_C
2_983650_A_G
2_983660_T_C

I've tried join and awk but somehow it doesn't seem to work. I suspect the fact that there's '_' on my second file.

Thank you

Upvotes: 1

Views: 87

Answers (4)

Thor
Thor

Reputation: 47189

I would go with paste and awk, e.g.:

paste file1 file2 | awk '{ $2 = $NF } NF--' OFS='\t'

Output:

2   2_983550_T_C    0   983550  T   C
2   2_983571_T_C    0   983571  T   C
2   2_983572_A_G    0   983572  A   G
2   2_983579_A_G    0   983579  A   G
2   2_983614_T_C    0   983614  T   C
2   2_983624_A_G    0   983624  A   G
2   2_983632_A_C    0   983632  A   C
2   2_983636_T_C    0   983636  T   C
2   2_983650_A_G    0   983650  A   G
2   2_983660_T_C    0   983660  T   C

Upvotes: 0

kvantour
kvantour

Reputation: 26531

I'm a bit puzzled why you need a second file. All information of file2 seems to be encoded in file1. You could just do something like this :

awk '{$2=$1"_"$4"_"$5"_"$6}1' file1

Upvotes: 2

ctac_
ctac_

Reputation: 2491

Your file2 have only one column so with awk.

awk -v f='file2' '{getline $2 <f}1' file1

If the separator of file2 is "_"

awk -v f='file2' '{getline a <f;split(a,b,"_");$2=b[1]}1' file1

Upvotes: 1

RavinderSingh13
RavinderSingh13

Reputation: 133700

EDIT: In case you want to make _ as field separator in Input_file2 then following may help you.

awk 'FNR==NR{a[FNR]=$1;next} (FNR in a){$2=a[FNR]} 1' FS="_" file2 FS=" " file1 | column -t

Following awk may help you here.

awk 'FNR==NR{a[FNR]=$0;next} (FNR in a){$2=a[FNR]} 1' file2 file1 | column -t

Upvotes: 1

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