CODEWITHSUNDEEP
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user1458512
user1458512

Reputation: 159

How to cut range of characters from multiple columns

I have a tab delimited file which looks like this:

CHROM <TAB> POS <TAB> AD0062-C <TAB> AD0063-C <TAB> AD0065-C <TAB> AD0074-C 
2L <TAB> 440 <TAB>0/1:63:60,0,249 <TAB>0/1:89:86,0,166 <TAB>1/1:96:107,24,0<TAB>1/1:49:42,6,0  
2L <TAB> 260<TAB>0/1:66:63,0,207<TAB> 1/1:99:227,111,0<TAB>1/1:99:255,144,0<TAB> 1/1:49:42,6,0
2L <TAB> 595 <TAB> 0/1:11:85,0,8 <TAB>0/1:13:132,0,10 <TAB>0/1:73:70,0,131<TAB> 0/1:59:72,0,56

I want to select only the first 3 characters starting from column 3 so that I can get an output that looks like this:

CHROM <TAB> POS <TAB> AD0062-C <TAB> AD0063-C <TAB> AD0065-C <TAB> AD0074-C 
2L <TAB> 440 <TAB> 0/1 <TAB> 0/1 <TAB> 1/1 <TAB> 1/1  
2L <TAB> 260 <TAB> 0/1 <TAB> 1/1 <TAB> 1/1 <TAB> 1/1
2L <TAB> 595 <TAB> 0/1 <TAB> 0/1 <TAB> 0/1 <TAB> 0/1

Thanks

Upvotes: 2

Views: 1724

Answers (3)

potong
potong

Reputation: 58430

This might work for you (GNU sed):

sed '1b;s/\(\S\{3\}\)\S*/\1/2g' file

Upvotes: 0

Birei
Birei

Reputation: 36262

One way using GNU sed. From second line until last one, substitute all characters between tabs with the first three at the beginning, and do it many times in each line but only from second match (avoiding first two fields):

sed '2,$ s/\([\t]...\)[^\t]*/\1/2g' infile

Output:

CHROM   POS     AD0062-C        AD0063-C        AD0065-C        AD0074-C 
2L      440     0/1     0/1     1/1     1/1
2L      260     0/1     1/1     1/1     1/1
2L      595     0/1     0/1     0/1     0/1

Upvotes: 0

Birei
Birei

Reputation: 36262

Using awk. For every line but first one and if it has more that two fields, get substring of them. The print command it is for every line because it has no condition.

awk '
    BEGIN { OFS = "\t" }
    NF > 2 && FNR > 1 { 
        for ( i=3; i<=NF; i++ ) { 
            $i = substr( $i, 1, 3 ) 
        } 
    } 
    { print }
' infile

Output:

CHROM   POS     AD0062-C        AD0063-C        AD0065-C        AD0074-C 
2L      440     0/1     0/1     1/1     1/1
2L      260     0/1     1/1     1/1     1/1
2L      595     0/1     0/1     0/1     0/1

Upvotes: 2

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