I am a new leaner and I am running a program with following script:
./Multiwfn >HF-Dr.out << EOF
HF.fchk
3
21
2
2
grep 'Global surface minimum:' HF-ESP.out | awk '{print $7,$8,$9,$7,$8,$9}'
EXIT
EOF
The output of this grep is something like:
0.043532 -0.032964 1.960094 0.043532 -0.032964 1.960094
I want to use the output of grep instead of input in the script, i.e. I want the script like:
./Multiwfn >HF-Dr.out << EOF
HF.fchk
3
21
2
2
0.043532 -0.032964 1.960094 0.043532 -0.032964 1.960094
EXIT
EOF
Is there any way that I hide (make non-executable) the grep input from my program and use only its output? Thank you in advance.
I do not understand the 'make non-executable' part of your question. As I understand it, you want it executed before it is given to ./Multiwfn.
There are several solutions:
1) PesaThe's comment:
./Multiwfn >HF-Dr.out << EOF
HF.fchk
3
21
2
2
$(grep 'Global surface minimum:' HF-ESP.out | awk '{print $7,$8,$9,$7,$8,$9}')
EXIT
EOF
2) Create the input in a pipe:
(echo -e "HF.fchk\n3\n21\n2\n2;grep 'Global surface minimum:' HF-ESP.out | awk '{print $7,$8,$9,$7,$8,$9}';echo EXIT) | ./Multiwfn >HF-Dr.out
3) use an intermediate file:
cat > file <<EOF
HF.fchk
3
21
2
2
EOF
grep 'Global surface minimum:' HF-ESP.out | awk '{print $7,$8,$9,$7,$8,$9}' >> file
echo EXIT >> file
./Multiwfn < file >HF-Dr.out
rm file
I'm sure that there are more ways, but this should put you on the right track.
Related
I am tasked with taking a file that has line entries that include string username=xxxx:
$ cat file.txt
Yadayada username=jdoe blablabla
Yadayada username=jdoe blablabla
Yadayada username=jdoe blablabla
Yadayada username=dsmith blablabla
Yadayada username=dsmith blablabla
Yadayada username=sjones blablabla
And finding how many times each user in the file shows up, which I can do manually by feeding username=jdoe for example:
$ grep -r "username=jdoe" file.txt | wc -l | tr -d ' '
3
What's the best way to report each user in the file, and the number of lines for each user, sorted from highest to lowest instances:
3 jdoe
2 dsmith
1 sjones
Been thinking of how to approach this, but drawing blanks, figured I'd check with our gurus on this forum. :)
TIA,
Don
In GNU awk:
$ awk '
BEGIN { RS="[ \n]" }
/=/ {
split($0,a,"=")
u[a[2]]++ }
END {
PROCINFO["sorted_in"]="#val_num_desc"
for(i in u)
print u[i],i
}' file
3 jdoe
2 dsmith
1 sjones
Using grep :
$ grep -o 'username=[^ ]*' file | cut -d "=" -f 2 | sort | uniq -c | sort -nr
Awk alone:
awk '
{sub(/.*username=/,""); sub(/ .*/,"")}
{a[$0]++}
END {for(i in a) printf "%d\t%s\n",a[i],i | "sort -nr"}
' file.txt
This uses awk's sub() function to achieve what grep -o does in other answers. It embeds the call to sort within the awk script. You could of course use that pipe after the awk script rather than within it if you prefer.
Oh, and unlike the other awk solutions presented here, this one (1) is portable to non-GNU-awk environments (like BSD, macOS) and doesn't depend on the username being in a predictable location on each line (i.e. $2).
Why might awk be a better choice than simpler tools like uniq? It probably wouldn't, for a super simple requirement like this. But good to have in your toolbox if you want something with the capability of a little more text processing.
Using sed, uniq, and sort:
sed 's/.*username=\([^ ]*\).*/\1/' file.txt | sort | uniq -c | sort -nr
If there are lines without usernames:
sed -n 's/.*username=\([^ ]*\).*/\1/p' input | sort | uniq -c | sort -nr
$ awk -F'[= ]' '{print $3}' file | sort | uniq -c | sort -nr
3 jdoe
2 dsmith
1 sjones
Following awk may help you on same too.
awk -F"[ =]" '{a[$3]++} END{for(i in a){print a[i],i | "sort -nr"}}' Input_file
I use egrep to output some lines with platform names:
XXX | egrep "i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$"
[30] i686-nptl-linux-gnu
[34] i686-w64-mingw32
[75] x86_64-unknown-linux-gnu
[77] x86_64-w64-mingw32
what I need is:
export PLATNUMS=30,34,75,77
How can I pipe the egrep command to sed / awk / bash script?
Try:
$ command | awk -F'[][ \t]+' '/i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$/{printf "%s%s",(f?",":"export PLATNUMS="),$2; f=1} END{print""}'
export PLATNUMS=30,34,75,77
How it works
-F'[][ \t]+'
Use any number of spaces, tabs, or [ or ] as field separators.
/i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$/{...}`
For the lines of interest, perform the commands in curly braces.
printf "%s%s",(f?",":"export PLATNUMS="),$2; f=1
For the lines of interest, print what we want.
The variable f marks whether this is the first line of interest.
END{print""}
After reading all lines, print a newline.
Creating a shell variable
export PLATNUMS=$(command | awk -F'[][ \t]+' '/i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$/{printf "%s%s",(f?",":""),$2; f=1} END{print""}')
For example, if the file input contains your data:
$ export PLATNUMS=$(awk -F'[][ \t]+' '/i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$/{printf "%s%s",(f?",":""),$2; f=1} END{print""}' input)
$ declare -p PLATNUMS
declare -x PLATNUMS="30,34,75,77"
For those who prefer their commands spread out over multiple lines:
export PLATNUMS=$(command | awk -F'[][ \t]+' '
/i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$/{
printf "%s%s",(f?",":""),$2
f=1
}
END{
print""
}
')
Perhaps this way, I can't try with your egrep.
export PLATNUMS=$(XXX | egrep "i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$" | sed ':A;s/\[\([[0-9]*\)].*/\1/;$bB;N;bA;:B;s/\n/,/g')
echo $PLATNUMS
How this work ?
Your egrep command return a multiline text
so sed read this text line by line this way
sed '
:A # label A
# here with your example
# on the first line the pattern space look like that
# [30] i686-nptl-linux-gnu
# on the second line the pattern space look like
# 30
# [34] i686-w64-mingw32
s/\[\([[0-9]*\)].*/\1/ # substitute all digit enclose by [] by only the digit
# on the first line the pattern space become
# 30
# on the second line the pattern space become
# 30
# 34
# and so on for each line
$bB # on the last line jump to B
N # get a newline in the pattern space
bA # It is not the last line so jump to A
:B # label B
# here we have read all the line
# the pattern space look like that without the #
# 30
# 34
# 75
# 77
s/\n/,/g' # subtitute all \n by a comma
# the pattern space become
# 30,34,75,77
# $(XXX | egrep .... | sed ...) return 30,34,75,77 in the variable PLATNUMS
# It is better not to use all capital letters in your variable name
With GNU sed and tr:
$ XXX | egrep "i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$" | sed -E 's,]\s+.+$,,g' | sed 's,^\[,,g' | tr '\n' ',' | sed -E 's,(^.+$),export PLATNUMS=\1,' | sed 's/,$//' && echo
I'm not sure what you want to achieve but you might want to automatically eval the output export:
$ eval $(XXX | egrep "i686-nptl-linux-gnu$|i686-w64-mingw32$|x86_64-unknown-linux-gnu$|x86_64-w64-mingw32$" | sed -E 's,]\s+.+$,,g' | sed 's,^\[,,g' | tr '\n' ',' | sed -E 's,(^.+$),export PLATNUMS=\1,' | sed 's/,$//' && echo)
$ echo $PLATNUMS
30,34,75,77
If you ever think you need grep+sed or 2 greps or 2 seds or any other combination then you should use 1 call to awk instead, and you never need grep or sed when you're using awk:
export PLATNUMS=$(XXX | awk -F'[][]' '/(i686-nptl-linux-gnu|i686-w64-mingw32|x86_64-unknown-linux-gnu|x86_64-w64-mingw32)$/{p=(p ? p "," : "") $2} END{print p}')
Btw in case it's useful, here's a couple of briefer regexps:
(i686-(nptl-linux-gnu|w64-mingw32)|x86_64-(unknown-linux-gnu|w64-mingw32))$
((i686-nptl|x86_64-unknown)-linux-gnu|(i686|x86_64)-w64-mingw32)$
and depending on your input data (since this will include combinations not provided by the above) you MIGHT only need:
(i686|x86_64)-(nptl|unknown|w64)-(linux-gnu|mingw32)$
The command 'grep -c blah *' lists all the files, like below.
% grep -c jill *
file1:1
file2:0
file3:0
file4:0
file5:0
file6:1
%
What I want is:
% grep -c jill * | grep -v ':0'
file1:1
file6:1
%
Instead of piping and grep'ing the output like above, is there a flag to suppress listing files with 0 counts?
SJ
How to grep nonzero counts:
grep -rIcH 'string' . | grep -v ':0$'
-r Recurse subdirectories.
-I Ignore binary files (thanks #tongpu, warlock).
-c Show count of matches. Annoyingly, includes 0-count files.
-H Show file name, even if only one file (thanks #CraigEstey).
'string' your string goes here.
. Start from the current directory.
| grep -v ':0$' Remove 0-count files. (thanks #LaurentiuRoescu)
(I realize the OP was excluding the pipe trick, but this is what works for me.)
Just use awk. e.g. with GNU awk for ENDFILE:
awk '/jill/{c++} ENDFILE{if (c) print FILENAME":"c; c=0}' *
Trying to grep a phrase out of multiple files as they are constantly populated (logs), but with hint as to which file was updated with the phrase.
For example:
grep bindaddr /vservers/*/var/log
gets me:
/vservers/11010/var/log:bindaddr=xxx.xxx.xxx.xxx
/vservers/12525/var/log:bindaddr=xxx.xxx.xxx.xxx
/vservers/12593/var/log:bindaddr=xxx.xxx.xxx.xxx
Which is cool, but I need this for tail -f.
tail -fn 100 /vservers/*/var/log | grep bindaddr
gets me the lines needed but no indicator in which file, so I need a mix of the two.
If you use -v in tail, you get a verbose mode: from man tab --> "always output headers giving file names". This way, whenever something happens in a file, you will get the header on the preceding line.
Together with this, you can use grep -B1 to show the match + the previous line.
All together, this should do:
tail -fvn 100 /vservers/*/var/log | grep -B1 bindaddr
Test
Doing this in one tab:
$ echo "hi" >> a2
$ echo "hi" >> a2
$ echo "hi" >> a1
$ echo "hi" >> a2
I got this in the other one:
$ tail -vfn 100 /tmp/a* | grep -B1 "h"
==> /tmp/a1 <==
==> /tmp/a2 <==
hi
hi
==> /tmp/a1 <==
hi
==> /tmp/a2 <==
hi
Something like this to put the filename in the front of each line from tail:
#!/bin/bash
# Arrange to kill all descendants on exit/interrupt
trap "kill 0" SIGINT SIGTERM EXIT
for f in *.txt; do
tail -f "$f" | sed "s/^/"$f": /" > /dev/tty &
done
# grep in stdin (i.e. /dev/tty)
grep bina -
I think some people are coming to this post looking for a way to display the filename while grepping the tail of multiple files:
for f in path/to/files*.txt; do echo $f; tail $f | grep 'SEARCH-THIS'; done;
This will display an output like this
filename1.txt
search result 1
search result 2
filenam2.txt
search result 3
search result 4
...
I would like to grep a specific word 'foo' inside specific files, then get the N lines around my match and show only the blocks that contain a second grep.
I found this but it doesn't really work...
find . | grep -E '.*?\.(c|asm|mac|inc)$' | \
xargs grep --color -C3 -rie 'foo' | \
xargs -n1 --delimiter='--' | grep --color -l 'bar'
For instance I have the file 'a':
a
b
c
d
bar
f
foo
g
h
i
j
bar
l
The file b:
a
bar
c
d
e
foo
g
h
i
j
k
I expect this for grep -c2 on both files because bar is contained in the -c2 range of foo. I do not get any match for ./bar because bar is not in the range -c2 of foo...
--
./foo- bar
./foo- f
./foo- **foo**
./foo- g
./foo- h
--
Any ideas?
You could do this pretty simply with a "while read line" loop:
find -regextype posix-extended -regex "./file[a-z]" | while read line; do grep -nHC2 "foo" $line | grep --color bar; done
Output:
./filea-5-bar
./filec-46-... host pwns.me [94.23.120.252]: 451 4.7.1 Local bar
configuration error ...
In this example, I created the following files:
filea - your example a
fileb - your example b
filec - some random exim log output with foo and bar tossed in 2 lines apart
filed - the same exim log output, but with foo and bar tossed in 3 lines apart
You could also pipe the output after done, to alter the format:
; done | sed 's/-([0-9]{1,6})-/: line: \1 ::: /'
Formatted output
./filea: line: 5 ::: bar
./filec: line: 46 ::: ... host pwns.me [94.23.120.252]: 451 4.7.1 Local bar configuration error ...
I think I only understand the first line of your question and this does what I think you mean!
#!/bin/bash
N=2
pattern1=a
pattern2=z
matchinglines=$(awk -v p="$pattern1" '$0~p{print NR}' file) # Generate array of matching line numbers
for x in ${matchinglines[#]}
do
((start=x-N))
[[ $start -lt 1 ]] && start=1 # Avoid passing negative line nmumbers to sed
((end=x+N))
echo DEBUG: Checking block between lines $start and $end
sed -ne "${start},${end}p" file | grep -q "$pattern2"
[[ $? -eq 0 ]] && sed -ne "${start},${end}p" file
done
You need to set pattern1 and pattern2 at the start of the script. It basically does some awk to build an array of the line numbers that match your first pattern. Then it loops through the array and sets the start and end range to +/-N either side of each matching line number. It then uses sed to extraact that block and passes it through grep to see if it contains pattern2 printing it if it does. It may not be the most efficient, but it is easy enough to understand and maintain.
It assumes your file is called file
pipe it twice
grep "[^foo\n]" | grep "\n{ntimes}foo\n{ntimes}"