Question 112568 in Ubuntu Question posted in
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Ubuntu – why is awk printing only first word in a field?

I have a tabulated .txt file with three fields, the third field often having multiple words:

GO:0000002  Akt3    mitochondrial genome maintenance
GO:0000002  Mef2a   mitochondrial genome maintenance
GO:0000002  Mgme1   mitochondrial genome maintenance
GO:0000002  Mpv17   mitochondrial genome maintenance
GO:0000002  Mrpl15  mitochondrial genome maintenance

I wanted to swap fields 1 and 2 using awk, but when i run the command:

awk 'BEGIN{OFS="t"}{print $2,$1,$3;}' file.txt

I get:

Akt3    GO:0000002  mitochondrial
Mef2a   GO:0000002  mitochondrial
Mgme1   GO:0000002  mitochondrial
Mpv17   GO:0000002  mitochondrial

Why do i not get all the words in the third field, and how to solve this?

Thanks in advance

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2

Answers


  1. 0

    You are printing 3 fields, that is why you only get 3 fields in the output. You are setting OFS to a tab but not FS.

    What you can do is flip only field 1 and field 2 using a variable like f1 to hold the field 1 value while switching the values.

    Then print the whole line adding 1 after the closing parenthesis to print the whole line. In case you have more columns you don’t have to manually specify them when printing.

    awk '
BEGIN{FS=OFS="t"}
{f1 = $1; $1 = $2; $2 = f1;}1
' file.txt

    Output

    Akt3    GO:0000002      mitochondrial genome maintenance
Mef2a   GO:0000002      mitochondrial genome maintenance
Mgme1   GO:0000002      mitochondrial genome maintenance
Mpv17   GO:0000002      mitochondrial genome maintenance
Mrpl15  GO:0000002      mitochondrial genome maintenance
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  2. 0

    There are various ways to solve the problem, but the main issue is that the output field separator has been set, but the default input field separator is both tabs & space. Setting them both to tab should give the output you want (or make it more generalizable by just swapping the first two fields & printing the remainder of the line)

    awk 'BEGIN{OFS="t"; FS="t";} {print $2,$1,$3;}' file.txt
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