CODEWITHSUNDEEP
bashsedwhile-loop
antoinefelden
antoinefelden

Reputation: 199

sed command within a while loop doesn't write output

I have this input file

gb|KY798440.1|
gb|KY842329.1|
MG082893.1
MG173246.1

and I want to get all the characters that are between the "|" or the full line if there is no "|". That is a desired output that looks like

KY798440.1
KY842329.1
MG082893.1
MG173246.1

I wrote:

while IFS= read -r line; do
    if [[ $line == *\|* ]] ; then
    sed 's/.*\|\(.*\)\|.*/\1/' <<< $line >> output_file
    else echo $line >> output_file
     fi
done < input_file

Which gives me

empty line
empty line
MG082893.1
MG173246.1

(note: empty line means an actual empty line - it doesn't actually writes "empty line")

The sed command works on a single example (i.e. sed 's/.*\|\(.*\)\|.*/\1/' <<< "gb|KY842329.1|" outputs KY842329.1) but within the loop it just does a line return. The else echo $line >> output_file seems to work.

Upvotes: 1

Views: 35

Answers (2)

William Pursell
William Pursell

Reputation: 212634

You could do

sed '/|/s/[^|]*|\([^|]*\)|.*/\1/' input

or

awk 'NF>1 {print $2} NF < 2 { print $1}' FS=\| input

or

sed -e 's/[^|]*|//' -e 's/|.*//' input

Upvotes: 0

James Brown
James Brown

Reputation: 37464

Bare sed:

$ sed 's/^[^|]*|\||[^|]*$//g' file

Output:

KY798440.1
KY842329.1
MG082893.1
MG173246.1

Upvotes: 2

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