How to find patterns across multiple lines using grep?

Question

I want to find files that have \"abc\" AND \"efg\" in that order, and those two strings are on different lines in that file. Eg: a file with content:

blah bl         


        

Answer 1

Sadly, you can't. From the grep docs:

grep searches the named input FILEs (or standard input if no files are named, or if a single hyphen-minus (-) is given as file name) for lines containing a match to the given PATTERN.

Answer 2

Grep is not sufficient for this operation.

pcregrep which is found in most of the modern Linux systems can be used as

pcregrep -M  'abc.*(\n|.)*efg' test.txt

where -M, --multiline allow patterns to match more than one line

There is a newer pcre2grep also. Both are provided by the PCRE project.

pcre2grep is available for Mac OS X via Mac Ports as part of port pcre2:

% sudo port install pcre2 

and via Homebrew as:

% brew install pcre

or for pcre2

% brew install pcre2

pcre2grep is also available on Linux (Ubuntu 18.04+)

$ sudo apt install pcre2-utils # PCRE2
$ sudo apt install pcregrep    # Older PCRE

Answer 3

With silver searcher:

ag 'abc.*(\n|.)*efg'

similar to ring bearer's answer, but with ag instead. Speed advantages of silver searcher could possibly shine here.

Answer 4

I used this to extract a fasta sequence from a multi fasta file using the -P option for grep:

grep -Pzo ">tig00000034[^>]+"  file.fasta > desired_sequence.fasta

• P for perl based searches
• z for making a line end in 0 bytes rather than newline char
• o to just capture what matched since grep returns the whole line (which in this case since you did -z is the whole file).

The core of the regexp is the [^>] which translates to "not greater than symbol"

Answer 5

While the sed option is the simplest and easiest, LJ's one-liner is sadly not the most portable. Those stuck with a version of the C Shell will need to escape their bangs:

sed -e '/abc/,/efg/\!d' [file]

This unfortunately does not work in bash et al.

Answer 6

The filepattern *.sh is important to prevent directories to be inspected. Of course some test could prevent that too.

for f in *.sh
do
  a=$( grep -n -m1 abc $f )
  test -n "${a}" && z=$( grep -n efg $f | tail -n 1) || continue 
  (( ((${z/:*/}-${a/:*/})) > 0 )) && echo $f
done

The

grep -n -m1 abc $f 

searches maximum 1 matching and returns (-n) the linenumber. If a match was found (test -n ...) find the last match of efg (find all and take the last with tail -n 1).

z=$( grep -n efg $f | tail -n 1)

else continue.

Since the result is something like 18:foofile.sh String alf="abc"; we need to cut away from ":" till end of line.

((${z/:*/}-${a/:*/}))

Should return a positive result if the last match of the 2nd expression is past the first match of the first.

Then we report the filename echo $f.