Insert filename as column, separated by a comma

Question

I have 100 file that looks like this

>file.csv
gene1,55
gene2,23
gene3,33

I want to insert the filename and make it look like this:

file.csv
gene1,55,file.csv
gene2,23,file.csv
gene3,33,file.csv

Now, I can almost get there using awk

awk '{print $0,FILENAME}' *.csv > concatenated_files.csv

But this prints the filenames with a space, instead of a comma. Is there a way to replace the space with a comma?

Sure, I just mean `bash` alone probably won't get you there. It's worth noting this is why Perl exists, though if you can depend on Python, Ruby, or whatever, I'd steer towards that instead for sure. — tadman, Oct 27 '22 at 15:32

score 1 · Accepted Answer · answered Oct 27 '22 at 16:19

1

Is there a way to replace the space with a comma?

Yes, change the OFS

$ awk -v OFS="," '{print $0,FILENAME}' file.csv
gene1,55,file.csv
gene2,23,file.csv
gene3,33,file.csv

answered Oct 27 '22 at 16:19

HatLess

score 0 · Answer 2 · answered Oct 27 '22 at 15:34

0

Figured it out, turns out:

for d in *.csv; do (awk '{print FILENAME (NF?",":"") $0}' "$d" > ${d}.all_files.csv); done

Works just fine.

answered Oct 27 '22 at 15:34

Workhorse

1

The parentheses are useless. there is no reason to run Awk in a subshell. – tripleee Oct 27 '22 at 15:43
1

this doesn't print `file.csv` on the first line (as displayed in expected output); this prints the filename at the beginning of each data line but in the expected output the filename is at the end of the data tlines – markp-fuso Oct 27 '22 at 16:20

score 0 · Answer 3 · answered Oct 27 '22 at 18:15

0

You can also create a new field

awk -vOFS=, '{$++NF=FILENAME}1' file.csv
gene1,55,file.csv
gene2,23,file.csv
gene3,33,file.csv

answered Oct 27 '22 at 18:15

3 Answers3