sed command within a while loop doesn't write output

Question

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.

Why use the while/read loop instead of just letting sed process the file? — William Pursell
– William Pursell, Commented Oct 21, 2020 at 22:05

James Brown · Accepted Answer · 2020-10-21 22:06:45Z

2

Bare sed:

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

Output:

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

answered Oct 21, 2020 at 22:06

James Brown

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1 Comment

antoinefelden Over a year ago

Oh that's embarrassing. I thought I tried that... Thanks though!!

William Pursell · Accepted Answer · 2020-10-21 22:09:36Z

0

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

answered Oct 21, 2020 at 22:09

William Pursell

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