CODEWITHSUNDEEP
linuxbashsed
user17063641
user17063641

Reputation:

How to replace "00" in data with "N/A" skipping first row in sed?

I'm working with GWAS data, My data looks like this:

IID,kgp11004425,rs11274005,kgp183005,rs746410036,kgp7979600
1,00,AG,GT,AK,00
32,AG,GG,AA,00,AT
300,TT,AA,00,AG,AA       
400,GG,AG,00,GT,GG

Desired Output:

IID,kgp11004425,rs11274005,kgp183005,rs746410036,kgp7979600
1,N/A,AG,GT,AK,N/A
32,AG,GG,AA,N/A,AT
98,TT,AA,N/A,AG,AA       
3,GG,AG,N/A,GT,GG

Here I'm trying to replace "00" with "N/A", but since I have 00 in the first_row/header_row and First column i.e IId, it's replacing here with N/A like kgp11N/A4425, rs11274N/A5,kgp183N/A5.... and Id column values with 300, 400, 500 as 3N/A, 4N/A, 5N/A. The bash command I used:

sed 's~00~N/A~g' allSNIPsFinaldata.csv

Can anyone please help "how not to include/Skip the first row or header row and first column and apply this effect. please help

Upvotes: 1

Views: 153

Answers (3)

The fourth bird
The fourth bird

Reputation: 163642

You might also skip the first row starting from the second one:

sed '2,$s~00~N/A~g' allSNIPsFinaldata.csv

If you don't want partial word matches, you can implement word boundaries around the 00 in different ways.

Upvotes: 0

Klaus Klein
Klaus Klein

Reputation: 81

You may specify an address to select the line(s) to apply the command to. Thus you might choose to exclude the first line like this:

sed '1!s~00~N/A~g' allSNIPsFinaldata.csv

As a sidenote I'd like to note that your example isn't actually CSV despite the file name; your header is comma-delimited but the rest of the file is using spaces.

Upvotes: 1

anubhava
anubhava

Reputation: 786359

With 2 capture groups you can use this sed:

sed -E 's~(^|[[:blank:]])00([[:blank:]]|$)~\1N/A\2~g' file

IID, kgp11004425, rs11274005, kgp183005, rs746410036, kgp7979600
1       N/A           AG        GT            AK          N/A
32      AG           GG        AA            N/A          AT
98      TT           AA        N/A            AG          AA
3       GG           AG        N/A            GT          GG

Details:

  • (^|[[:blank:]]): Match start or a whitespace in capture group #1
  • 00: Match 00
  • ([[:blank:]]|$): Match end or a whitespace in capture group #2
  • \1N/A\2: Replacement to put back value of capture group #1 followed by N/A followed by value of capture group #2

Upvotes: 2

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