sed - unterminated `s' command - bash

Question

I have this peace of code:
cat BP.csv | while read line ; do
goterm=$(awk '{print $1}') ;
name=$(awk '{print $2}') ;
grep -w "$goterm" GOEA.csv | sed "s/$goterm/pi/g" ;
done
file BP.csv has this format:
GO:0008283 cell proliferation
GO:0009405 pathogenesis
GO:0010201 response to continuous far red light stimulus by the high-irradiance response system
GO:0009641 shade avoidance
while GOEA.csv has this format:
4577 GO:0006807 0.994 2014_06_01
4577 GO:0016788 0.989 2014_06_01
4577 GO:0043169 0.977 2014_06_01
4577 GO:0043170 0.963 2014_06_01
sed doesn't work. I want to change GO:0043170 for example, to string "pi", but it gives:
sed: -e expression #1, char 12: unterminated `s' command
Why?
Thanks.

Answer 1

You running your awk command against no input, Try this:
cat BP.csv | while read line ; do
goterm=$(awk '{print $1}' <<< "$line") ;
name=$(awk '{print $2}' <<< "$line" ) ;
grep -w "$goterm" GOEA.csv | sed "s/$goterm/pi/g" ;
done

Answer 2

Let's clean up this code a bit:
while read goterm name
do
grep -w "$goterm" GOEA.csv | sed "s/$goterm/pi/g"
done < BP.cvs
The problem is that your awk statements are attempting to read in from STDIN just like your while is doing. You're reading from the same input stream.
What you want to do is to pull out the values from your line. I'm using read to do this. The read statement uses the values in $IFS to separate out the input. This is normally spaces, tabs, and newlines. The read reads each variable you put on the line, and the last value read in contains the entire rest of the line.
Thus:
while read line
reads in the entire line while:
while goterm name
will break the line as
goterm="GO:0008283"
name="cell proliferation"
One more thing. When you use grep and sed together, you probably can get away with just sed:
while read goterm name
do
sed -n "/$goterm/s/$goterm/pi/gp" GOEA.csv
done < BP.csv
The format for the sed command is:
/lines/command/parameters/
So, I'm searching for lines with $goterm in them, then I am replacing $goterm with pi. The -n means don't print out the lines as sed processes them and p means to print out the lines were the substitute is located.
By the way, csv as a file suffix means comma separated values but neither file looks like it is comma separated. Are these tabs separating each field. If so, you'll need to modify $IFS to be tabs.

Answer 3

I would restructure that whole thing more like this:
while read goterm restofline
do
grep -w "${goterm}" GOEA.csv | sed -e "s/${goterm}/pi/g"
done < BP.csv
No reason for the awk things, as the bash read builtin will do rudimentary field splitting for you if you give it multiple variables. Also, you aren't using name anyway, so it's not needed. cat is unnecessary as well.
Depending on your exact use case, even the grep may be unnecessary, making the inner command simply sed -ne "s/${goterm}/pi/gp" GOEA.csv. Unless your purpose for the grep -w is eliminating lines where ${goterm} is a substring of a word instead of the whole word...
For future reference, inserting a set -x above your loop in your script would show you the exact commands that are being run, so that you can compare them with your expectations.