CODEWITHSUNDEEP
bashcsv
kbw
kbw

Reputation: 35

Ignore commas within a bash variable that is sent to a csv file

I'm having trouble ignoring the commas within a bash variable so that the csv file doesn't split up the variable into different columns. If the variable were "TACGTAT,TACG", I would want that as a single column instead of two different columns.

Here is my full script:

for filename in "$1"/*.vcf; do
  bcftools query -f '%POS %REF %ALT\n' "$filename" > temp_reads.txt
  echo "Sick Read!: "$(cat temp_reads.txt)""
  echo ""$(basename "$filename")","$(cat temp_reads.txt)"" >> output.csv
done

And I specifically want everything in the "$(cat temp_reads.txt)" expansion to be included as a single column in the csv file in case there happened to be a comma in there.

Thanks!

Upvotes: 0

Views: 1331

Answers (2)

tripleee
tripleee

Reputation: 189387

The wrangling of temporary files is completely unnecessary anyway.

for filename in "$1"/*.vcf; do
  bcftools query -f '%POS %REF %ALT\n' "$filename" |
  sed "s/^/$(basename "$filename"),/"
done >output.csv

Generally speaking, you cannot nest double quotes: ""foo is just an unquoted foo with an empty quoted string to its left (which of course disappears entirely by the time the shell is done parsing this expression).

Notice also how moving the redirection after the done improves legibility and efficiency. Because you only redirect once, you can write instead of append (assuming you don't need to append for other reasons, of course) and you don't open, seek to the end of the file, write, and close every time through the loop, so you save a fair bit on the I/O overhead.

Upvotes: 1

Walter A
Walter A

Reputation: 20002

Testdata:

echo 'a,b and "c".' > temp_reads.txt
filename="What a lovely name"

Incorrect solution ignoring double quotes in the file

printf '"%s","%s"\n' "${filename}" "$(cat temp_reads.txt)"

Escaping each double quote with a second one in file 

sed 's/"/""/g' temp_reads.txt

Combined

printf '"%s","%s"\n' "${filename}" "$(sed 's/"/""/g' temp_reads.txt)"

Upvotes: 0

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