Manipulating column text in unix

Question

I have a tab delimited text file like this-

test.txt

chrom1  start1  end1
    2   8828280 8828281
    2   8828952 8828953
    2   115627275   115627276
    3   63945545    63945546
    3   109753479   109753480
    3   109753640   109753641
    4   31116488    31116489
    4   31116523    31116524

How can I do the following tasks in a unix shell-

change the column name "chrom1" to "chr" and
add "chr" in front of the each values in column "chr".

The output should look like -

 chr    start1  end1
 chr2   8828280 8828281
 chr2   8828952 8828953
 chr2   115627275   115627276
 chr3   63945545    63945546
 chr3   109753479   109753480
 chr3   109753640   109753641
 chr4   31116488    31116489
 chr4   31116523    31116524

anubhava · Accepted Answer · 2016-08-04 16:53:37Z

1

You can use awk:

awk 'BEGIN{FS=OFS="\t"} {$1 = "chr" (NR==1 ? "" : $1)} 1' file

chr   start1     end1
chr2  8828280    8828281
chr2  8828952    8828953
chr2  115627275  115627276
chr3  63945545   63945546
chr3  109753479  109753480
chr3  109753640  109753641
chr4  31116488   31116489
chr4  31116523   31116524

edited Aug 4, 2016 at 16:53

answered Aug 4, 2016 at 16:32

anubhava

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5 Comments

panbar Over a year ago

Thanks @anubhava. If I want to do the same two changes also on column 4 of the same file, could you suggest how to do that?

anubhava Over a year ago

Sorry I don't understand as your question only mentions first column.

panbar Over a year ago

If the changes have to be made on column 4 instead of column 1.

anubhava Over a year ago

Just change $1 to $4 as awk 'BEGIN{FS=OFS="\t"} {$4 = "chr" (NR==1 ? "" : $4)} 1' file

Claes Wikner Over a year ago

I think OFS="\t" is enough otherwise first column does not look alright.

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