Chris_Rands Chris_Rands - 1 month ago 9
Bash Question

Why is grep so slow and memory intensive with -w (--word-regexp) flag?

I have a list of ids in a file and a data file (of ~3.2Gb in size), and I want to extract the lines in the data file that contain the id and also the next line. I did the following:

grep -A1 -Ff file.ids file.data | grep -v "^-" > output.data


This worked, but also extracted unwanted substrings, for example if the id is
EA4
it also pulled out the lines with
EA40
.

So I tried using the same command but adding the
-w
(
--word-regexp
) flag to the first
grep
to match whole words. However, I found my command now ran for >1 hour (rather than ~26 seconds) and also started using 10s of gigabytes of memory, so I had to kill the job.

Why did adding
-w
make the command so slow and memory grabbing? How can I efficiently run this command to get my desired output? Thank you

file.ids
looks likes this:

>EA4
>EA9


file.data
looks like this:

>EA4 text
data
>E40 blah
more_data
>EA9 text_again
data_here


output.data
would look like this:

>EA4 text
data
>EA9 text_again
data_here

Answer

grep -F string file is simply looking for occurrences of string in the file but grep -w -F string file has to check each character before and after string too to see if they are word characters or not. That's a lot of extra work and one possible implementation of it would be to first separate lines into every possible non-word-character-delimited string with overlaps of course so that could take up a lot of memory but idk if that's what's causing your memory usage or not.

In any case, grep is simply the wrong tool for this job since you only want to match against a specific field in the input file, you should be using awk instead:

$ awk 'NR==FNR{ids[$0];next} /^>/{f=($1 in ids)} f' file.ids file.data
>EA4 text
data
>EA9 text_again
data_here

The above assumes your "data" lines cannot start with >. If they can then tell us how to identify data lines vs id lines.

Note that the above will work no matter how many data lines you have between id lines, even if there's 0 or 100:

$ cat file.data
>EA4 text
>E40 blah
more_data
>EA9 text_again
data 1
data 2
data 3

$ awk 'NR==FNR{ids[$0];next} /^>/{f=($1 in ids)} f' file.ids file.data
>EA4 text
>EA9 text_again
data 1
data 2
data 3

Also, you don't need to pipe the output to grep -v:

grep -A1 -Ff file.ids file.data | grep -v "^-" > output.data

just do it all in the one script:

awk 'NR==FNR{ids[$0];next} /^>/{f=($1 in ids)} f && !/^-/' file.ids file.data