Is there a way to change comma to underscore within a quoted field (delimiter = ,)

Asked Jul 12 '19 at 13:16

Active Jul 12 '19 at 13:25

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I have a csv file. There are fields within this csv file containing quotes. And within these quotes there could be commas available, this is not always the case. If I extract a column using:

awk -F, '{ print $3 }' testfile.csv

This won't work. So my idea is to change the , within the quoted field to _ and 'escape' the problem.

This is the contents of my file:

chromosome,position,marker,sample1,sample2
chr1,100,NA,A,C
chr1,200,"test1,test2",A,C
chr1,300,NA,A,C
chr1,400,"test6",A,C
chr1,500,NA,A,C
chr1,600,"test3,test4,test5",A,C

My desired contents would be:

chromosome,position,marker,sample1,sample2
chr1,100,NA,A,C
chr1,200,"test1_test2",A,C
chr1,300,NA,A,C
chr1,400,"test6",A,C
chr1,500,NA,A,C
chr1,600,"test3_test4_test5",A,C

Any suggestions?

edited Jul 12 '19 at 13:25

Inian

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asked Jul 12 '19 at 13:16

Slartibartfast

Do you need to replace `,` by `_` in quoted strings or do you need to extract the third column from your CSV file ? In the latter case, I would use [python](https://docs.python.org/3/library/csv.html) instead of awk – mouviciel Jul 12 '19 at 13:24
I'd like to have the entire row, not the third column – Slartibartfast Jul 12 '19 at 13:27
In the former case, I would split lines with `"` as field separator and replace `,` by `_` only in even columns. – mouviciel Jul 12 '19 at 13:28
Your awk command does not output the entire row, only the third column – mouviciel Jul 12 '19 at 13:29
This I know (of course :) ) but this was to visualize that problem with the commas within quotes. – Slartibartfast Jul 12 '19 at 13:32
I think this is enough "awk '{gsub(/,test/,"_test")}1' file" – Claes Wikner Jul 12 '19 at 16:20

Is there a way to change comma to underscore within a quoted field (delimiter = ,)

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