Pattern exclusion between two files

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# 1  
Old 03-03-2014
Pattern exclusion between two files

I have a large file (file1) that has 96770154 lines and a smaller file (file2) that has 3 lines. I want to remove all of the strings from file1 that occur in file2.

file1 looks like this:


file2 looks like this:


The output should look like this:


What I have so far is this but the output is not 2 lines. It is instead 6 lines for whatever reason that I'm not understanding:

while read A B; do grep -v $A file1; done < file2 > out

Last edited by Scrutinizer; 03-03-2014 at 04:30 AM.. Reason: typos; [mod] quote tags to code tags
# 2  
Old 03-03-2014
Try the below
awk '{if(NR == FNR) {a[$0]} else {for (x in a) {if($0 ~ x) {print $0; next}}}}' file2 file1

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# 3  
Old 03-03-2014
The while loop will call grep three times with a grep -v YES a grep -v NO and a grep -v GOOD and that output is concatenated.

Alternatively you could try without a while loop with:
grep -vf file2 file1


will be left out since it has the string "NO" in it..
This User Gave Thanks to Scrutinizer For This Post:
# 4  
Old 03-03-2014
any way to output each of the output lines into their own separate files?
# 5  
Old 03-03-2014
You mean every line of the output is a separate file?
grep -vf file2 file1 | split -l 1

# 6  
Old 03-03-2014
all those match YES will go to output_YES, NO will go to output_NO...
but, if a string has both YES & NO, the below code will only send the line to output_YES.
awk '{if(NR == FNR) {a[$0]} else {for (x in a) {if($0 ~ x) {print $0 > "output_" x; next}}}}' file2 file1

If you want the string that contains both YES and NO to be sent to both the output file, use the below
awk '{if(NR == FNR) {a[$0]} else {for (x in a) {if($0 ~ x) {print $0 > "output_" x}}}}' file2 file1

# 7  
Old 03-03-2014
This isn't quite what I mean. In general if I have a while loop

while read A B ; do 
    something else file1
done; < file2 > out

How can I output a file each time the while loop goes through 1 cycle. The length of the output can vary so I can't use
split -l 1

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