How to make "grep" output complete word that includes the match? - grep

I would like grep to print out all complete words that include the match.
Google did not help me. Here what I tried:
cat file.txt
21676 Mm.24685 NM_009346 ENSMUSG00000055320
20349 Mm.134093 NM_011348 ENSMUSG00000063531
12456 Mm.134000 NM_011228 GM415666
grep -o "ENSMUS" file.txt
ENSMUS
ENSMUS
Desired output:
ENSMUSG00000055320
ENSMUSG00000063531
Thanks for your help!

You may use:
grep -wo "ENSMUS[^[:blank:]]*" file.txt
ENSMUSG00000055320
ENSMUSG00000063531
Here [^[:blank:]]* will match 0 or more characters that are not whitespaces. -w will ensure full word matches.

To extract ENSEMBL mouse accession numbers without the version number:
grep -Po 'ENSMUS\w+' in_file
With the version number:
grep -Po 'ENSMUS\S+' in_file
Here,
\w+ : 1 or more word characters ([A-Za-z0-9_]).
\S+ : 1 or more non-whitespace characters (you can also be more restrictive and use [\w.]+, which is 1 or more word character or literal dot).
Here, GNU grep uses the following options:
-P : Use Perl regexes.
-o : Print the matches only (1 match per line), not the entire lines.
SEE ALSO:
grep manual
perlre - Perl regular expressions

Related

Regex for line containing one or more spaces or dashes

I got .txt file with city names, each in separate line. Some of them are few words with one or multiple spaces or words connected with '-'. I need to create bash command which will echo those lines out. Currently I'm using cat piped with grep but I can't get both spaces and dash into one search and I had problems with checking for multiple spaces.
print lines with dash:
cat file.txt | grep ".*-.*"
print lines with spaces:
cat file.txt | grep ".*\s.*"
tho when I try to do:
cat file.txt | grep ".*\s+.*"
I get nothing.
Thanks for help
Something like that should work:
grep -E -- ' |\-' file.txt
Explanation:
-E: to interpret patterns as extended regular expressions
--: to signify the end of command options
' |\-': the line contains either a space or a dash
This does not directly address your question, but is too much to put in a comment.
You don't need the .* in your patterns. .* at the beginning or end of a pattern is useless, because it means "0 or more of any character" and so will always match.
These lines are all identical:
cat file.txt | grep ".*-.*"
cat file.txt | grep "-.*"
cat file.txt | grep "-"
Plus you don't need to cat and pipe:
grep "-" file.txt
When grep pattern matches, the default action is to print the whole line, so .* in all your patterns are redundant, you may delete them. Also, you don't have to use cat file | as you may specify the file to grep directly after pattern, i.e. grep 'pattern' file.txt.
Here are some more details:
grep ".*-.*" = grep -- "-" - returns any lines having a - char (-- singals the end of options, the next thing is the pattern)
grep ".*\s.*" = grep "\s" - matches and returns lines containing a whitespace char (only GNU grep)
grep ".*\s+.*" = grep "\s+" - returns line containing a whitespace followed with a literal + char (since you are using POSIX BRE regex here the unescaped + matches a literal plus symbol).
You want
grep "[[:space:]-]" file.txt
See the online demo:
#!/bin/bash
s='abc - def
ghi
jkl mno'
grep '[[:space:]-]' <<< "$s"
Output:
abc - def
jkl mno
The [[:space:]-] POSIX BRE and ERE (enabled with -E option) compliant pattern matches either any whitespace (with the [:space:] POSIX character class) or a hyphen.
Note that [\s-] won't work since \s inside a bracket expression is not treated as a regex escape sequence but as a mere \ or s.

grep 3rd keyword from a string seperated by '-'

My hostname details are as below after showing command of hostname in linux
my-host-test-db-10001.dns.biz.xyz.com
my-host-test2-db-10002.dns.biz.xyz.com
my-host-test3-db-10003.dns.biz.xyz.com
I want to fetch the 3rd string from these above (test/test2/test3). how can I achieve it?
In addition to the simpler solution using cut, you can use more flexible grep:
hostname | grep -Po '^[^-]+-[^-]+-\K[^-]+'
For example:
grep -Po '^[^-]+-[^-]+-\K[^-]+' <<< 'my-host-test2-db-10002.dns.biz.xyz.com'
Output:
test2
Here, GNU grep uses the following options:
-P : Use Perl regexes.
-o : Print the matches only (1 match per line), not the entire lines.
\K : Cause the regex engine to "keep" everything it had matched prior to the \K and not include it in the match. Specifically, ignore the preceding part of the regex when printing the match.
SEE ALSO:
perlre - Perl regular expressions

Cutting a length of specific string with grep

Let's say we have a string "test123" in a text file.
How do we cut out "test12" only or let's say there is other garbage behind "test123" such as test123x19853 and we want to cut out "test123x"?
I tried with grep -a "test123.\{1,4\}" testasd.txt and so on, but just can't get it right.
I also looked for example, but never found what I'm looking for.
expr:
kent$ x="test123x19853"
kent$ echo $(expr "$x" : '\(test.\{1,4\}\)')
test123x
What you need is -o which print out matched things only:
$ echo "test123x19853"|grep -o "test.\{1,4\}"
test123x
$ echo "test123x19853"|grep -oP "test.{1,4}"
test123x
-o, --only-matching show only the part of a line matching PATTERN
If you are ok with awkthen try following(not this will look for continuous occurrences of alphabets and then continuous occurrences of digits, didn't limit it to 4 or 5).
echo "test123x19853" | awk 'match($0,/[a-zA-Z]+[0-9]+/){print substr($0,RSTART,RLENGTH)}'
In case you want to look for only 1 to 4 digits after 1st continuous occurrence of alphabets then try following(my awk is old version so using --re-interval you could remove it in case you have latest version of ittoo).
echo "test123x19853" | awk --re-interval 'match($0,/[a-zA-Z]+[0-9]{1,4}/){print substr($0,RSTART,RLENGTH)}'

How to grep for a 7 digit hexadecimal string and return only that hexadecimal string?

I am trying to extract all the leading 7 digit hexadecimal strings in a file, that contains lines such as:
3fce110:: ..\Utilities\c\misc.c(431): YESFREED (120 bytes) Misc
egrep -o '^[0-9a-f]{7}\b' file.txt
egrep is the same as grep -E; it uses extended regexp.
-o prints only the matching part of each line.
^ anchors the match to the beginning of the line.
[0-9a-f]{7} matches seven hexadecimal characters. If you want to match uppercase letters add A-F here or add the -i flag.
\b checks for a word boundary; it ensures we don't match hex numbers more than 7 digits long.
If all the lines in the file follow the given format then a couple of methods:
$ grep -o '^[^:]*' file
3fce110
$ awk -F: '{print $1}' file
3fce110
$ cut -d: -f1 file
3fce110
$ sed  's/:.*//' file
3fce110

Can grep show only words that match search pattern?

Is there a way to make grep output "words" from files that match the search expression?
If I want to find all the instances of, say, "th" in a number of files, I can do:
grep "th" *
but the output will be something like (bold is by me);
some-text-file : the cat sat on the mat
some-other-text-file : the quick brown fox
yet-another-text-file : i hope this explains it thoroughly
What I want it to output, using the same search, is:
the
the
the
this
thoroughly
Is this possible using grep? Or using another combination of tools?
Try grep -o:
grep -oh "\w*th\w*" *
Edit: matching from Phil's comment.
From the docs:
-h, --no-filename
Suppress the prefixing of file names on output. This is the default
when there is only one file (or only standard input) to search.
-o, --only-matching
Print only the matched (non-empty) parts of a matching line,
with each such part on a separate output line.
Cross distribution safe answer (including windows minGW?)
grep -h "[[:alpha:]]*th[[:alpha:]]*" 'filename' | tr ' ' '\n' | grep -h "[[:alpha:]]*th[[:alpha:]]*"
If you're using older versions of grep (like 2.4.2) which do not include the -o option, then use the above. Else use the simpler to maintain version below.
Linux cross distribution safe answer
grep -oh "[[:alpha:]]*th[[:alpha:]]*" 'filename'
To summarize: -oh outputs the regular expression matches to the file content (and not its filename), just like how you would expect a regular expression to work in vim/etc... What word or regular expression you would be searching for then, is up to you! As long as you remain with POSIX and not perl syntax (refer below)
More from the manual for grep
-o Print each match, but only the match, not the entire line.
-h Never print filename headers (i.e. filenames) with output lines.
-w The expression is searched for as a word (as if surrounded by
`[[:<:]]' and `[[:>:]]';
The reason why the original answer does not work for everyone
The usage of \w varies from platform to platform, as it's an extended "perl" syntax. As such, those grep installations that are limited to work with POSIX character classes use [[:alpha:]] and not its perl equivalent of \w. See the Wikipedia page on regular expression for more
Ultimately, the POSIX answer above will be a lot more reliable regardless of platform (being the original) for grep
As for support of grep without -o option, the first grep outputs the relevant lines, the tr splits the spaces to new lines, the final grep filters only for the respective lines.
(PS: I know most platforms by now would have been patched for \w.... but there are always those that lag behind)
Credit for the "-o" workaround from #AdamRosenfield answer
It's more simple than you think. Try this:
egrep -wo 'th.[a-z]*' filename.txt #### (Case Sensitive)
egrep -iwo 'th.[a-z]*' filename.txt ### (Case Insensitive)
Where,
egrep: Grep will work with extended regular expression.
w : Matches only word/words instead of substring.
o : Display only matched pattern instead of whole line.
i : If u want to ignore case sensitivity.
You could translate spaces to newlines and then grep, e.g.:
cat * | tr ' ' '\n' | grep th
Just awk, no need combination of tools.
# awk '{for(i=1;i<=NF;i++){if($i~/^th/){print $i}}}' file
the
the
the
this
thoroughly
grep command for only matching and perl
grep -o -P 'th.*? ' filename
I was unsatisfied with awk's hard to remember syntax but I liked the idea of using one utility to do this.
It seems like ack (or ack-grep if you use Ubuntu) can do this easily:
# ack-grep -ho "\bth.*?\b" *
the
the
the
this
thoroughly
If you omit the -h flag you get:
# ack-grep -o "\bth.*?\b" *
some-other-text-file
1:the
some-text-file
1:the
the
yet-another-text-file
1:this
thoroughly
As a bonus, you can use the --output flag to do this for more complex searches with just about the easiest syntax I've found:
# echo "bug: 1, id: 5, time: 12/27/2010" > test-file
# ack-grep -ho "bug: (\d*), id: (\d*), time: (.*)" --output '$1, $2, $3' test-file
1, 5, 12/27/2010
cat *-text-file | grep -Eio "th[a-z]+"
You can also try pcregrep. There is also a -w option in grep, but in some cases it doesn't work as expected.
From Wikipedia:
cat fruitlist.txt
apple
apples
pineapple
apple-
apple-fruit
fruit-apple
grep -w apple fruitlist.txt
apple
apple-
apple-fruit
fruit-apple
I had a similar problem, looking for grep/pattern regex and the "matched pattern found" as output.
At the end I used egrep (same regex on grep -e or -G didn't give me the same result of egrep) with the option -o
so, I think that could be something similar to (I'm NOT a regex Master) :
egrep -o "the*|this{1}|thoroughly{1}" filename
To search all the words with start with "icon-" the following command works perfect. I am using Ack here which is similar to grep but with better options and nice formatting.
ack -oh --type=html "\w*icon-\w*" | sort | uniq
You could pipe your grep output into Perl like this:
grep "th" * | perl -n -e'while(/(\w*th\w*)/g) {print "$1\n"}'
grep --color -o -E "Begin.{0,}?End" file.txt
? - Match as few as possible until the End
Tested on macos terminal
$ grep -w
Excerpt from grep man page:
-w: Select only those lines containing matches that form whole words. The test is that the matching substring must either be at the beginning of the line, or preceded by a non-word constituent character.
ripgrep
Here are the example using ripgrep:
rg -o "(\w+)?th(\w+)?"
It'll match all words matching th.

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