CODEWITHSUNDEEP
bashgrep
jensG
jensG

Reputation: 43

Concatenate grep output string (bash script)

I'm processing some data from a text file using a bash script (Ubuntu 12.10).

The basic idea is that I select a certain line from a file using grep. Next, I process the line to get the number with sed. Both the grep and sed command are working. I can echo the number.

But the concatenation of the result with a string goes wrong.

I get different results when combining string when I do a grep command from a variable or a file. The concatenation goes wrong when I grep a file. It works as expected when I grep a variable with the same text as in the file.

What am I doing wrong with the grep from a file?

Contents of test.pdb

REMARK overall = 324.88  
REMARK bon     = 24.1918  
REMARK coup    = 0

My script

#!/bin/bash

#Correct function
echo "Working code"
TEXT="REMARK overall = 324.88\nREMARK bon     = 24.1918\nREMARK coup    = 0\n"
DATA=$(echo -e $TEXT | grep 'overall' | sed -n -e "s/^.*= //p" )

echo "Data: $DATA"
DATA="$DATA;0"
echo $DATA


#Not working
echo ""
echo "Not working code"
DATA=$(grep 'overall' test.pdb | sed -n -e "s/^.*= //p")

echo "Data: $DATA"
DATA="$DATA;0"
echo $DATA

Output

Working code
Data: 324.88
324.88;0

Not working code
Data: 324.88
;04.88

Upvotes: 4

Views: 14406

Answers (3)

Salvatore
Salvatore

Reputation: 36

I went crazy with the same issue.

The real problem is that your "test.pdb" has probably a wrong EOL (end of line) character.

Linux EOL: LF (aka \n)

Windows EOL: CR LF (aka \r \n)

This mean that echo and grep will have problem with this extra character (\r), luckily tr, sed and awk manage it correctly.

So you can try also with:

DATA=$(grep 'overall' test.pdb | sed -n -e "s/^.*= //p" | sed -e 2s/\r$//")

or

DATA=$(grep 'overall' test.pdb | sed -n -e "s/^.*= //p" | tr -d '\r')

Upvotes: 2

Amir Afghani
Amir Afghani

Reputation: 38511

Try this:

SUFFIX=";0"
DATA="${DATA}${SUFFIX}"

Upvotes: 0

Gilles Quénot
Gilles Quénot

Reputation: 184955

With , it will be more reliable and cleaner I guess :

$ awk '$2=="overall"{print "Working code\nData: " $4 "\n" $4 ";0"}' file.txt
Working code
Data: 324.88
324.88;0

Upvotes: 0

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