Swap value in column 1

Question

I have a file that looks like this:

CHROM POS ID REF ALT
22 345 567 A G
22 454 666 T G
23 454 555 C C
23 565 777 G G

And I want to change it to:

CHROM POS ID REF ALT
22 345 567 A G
22 454 666 T G
X 454 555 C C
X 565 777 G G

i.e. In column 1, I want to swap 23 with X. How can I do this?

Thanks.

janos · Accepted Answer · 2014-01-07T21:40:25.863

3

In GNU sed you could do like this:

sed -e 's/^23\>/X/' file.txt

Or using perl:

perl -pe 's/^23\b/X/' file.txt

Or using awk:

awk '{ if ($1 == 23) sub("23", "X"); print }' file.txt

If you want to update the file after the replacement, then you can use any of these commands:

sed -i -e 's/^23\>/X/' file.txt
perl -pi -e 's/^23\b/X/' file.txt

edited Jan 07 '14 at 21:40

answered Jan 07 '14 at 21:32

janos

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score 2 · Answer 2 · edited May 23 '17 at 12:11

2

Do you have access to any scripting languages? a perl or python script to replace a line start followed by 23 with a line start followed by X would be pretty simple.

see this answer: Find and Replace Inside a Text File from a Bash Command

so something like...

perl -pi -e 's/^23\s/X /g' /tmp/file.txt

edited May 23 '17 at 12:11

Community

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answered Jan 07 '14 at 21:34

AJAX86

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why do you match with `\n` instead of `^` (beginning of line)? – ShinTakezou Jan 07 '14 at 21:37
good catch. that would be the correct method. My original answer would miss items on line one. – AJAX86 Jan 07 '14 at 21:40
also, are you sure about sub string `X\s`? it won't re-add the space between 23 and the 454 or whatever – ShinTakezou Jan 07 '14 at 21:43

Swap value in column 1

2 Answers2