Text file to be searched (input.txt):
GREEN TREE CONIFER
GREEN BUSH BERRY
RED LEAF MAPLE
RED TRUNK MAPLE
Input pattern file; one word per line (patterns.txt):
GREEN
MAPLE
Desired output:
GREEN TREE CONIFER
RED LEAF MAPLE
My command:
$ grep -m1 -f patterns.txt input.txt
However, this only returns:
GREEN TREE CONIFER
How should I modify my command to get only the first match, from each pattern in the patterns.txt file?
I haven't come up with a single grep invokation solution.
Here I propose a loop to get first occurence for each pattern in input file.
p=$(cat pattern.txt)
for x in $(seq $(echo "$p" | wc -l)); do
cat input.txt | grep -m 1 "$(echo "$p" | head -n $x | tail -n 1)"
done
Related
I have a space-separated file that looks like this:
$ cat in_file
GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1 Chal_sti_synt_C
GCF_000046845.1_ASM4684v1_protein.faa WP_004927566.1 Chal_sti_synt_C
GCF_000046845.1_ASM4684v1_protein.faa WP_004919950.1 FAD_binding_3
GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1 FAD_binding_3
I am using the following shell script utilizing grep to search for strings:
$ cat search_script.sh
grep "GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1" Pfam_anntn_temp.txt
grep "GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1" Pfam_anntn_temp.txt
The problem is that I want each grep command to return only the first instance of the string it finds exclusive of the previous identical grep command's output.
I need an output which would look like this:
$ cat out_file
GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1 Chal_sti_synt_C
GCF_000046845.1_ASM4684v1_protein.faa WP_004920342.1 FAD_binding_3
in which line 1 is exclusively the output of the first grep command and line 2 is exclusively the output of the second grep command. How do I do it?
P.S. I am running this on a big file (>125,000 lines). So, search_script.sh is mostly composed of unique grep commands. It is the identical commands' execution that is messing up my downstream analysis.
I'm assuming you are generating search_script.sh automatically from the contents of in_file. If you can count how many times you'll repeat the same grep command you can just use grep once and use head, for example if you know you'll be using it 2 times:
grep "foo" bar.txt | head -2
Will output the first 2 occurrences of "foo" in bar.txt.
If you have to do the grep commands separately, for example if you have other code in between the grep commands, you can mix head and tail:
grep "foo" bar.txt | head -1 | tail -1
Some other commands...
grep "foo" bar.txt | head -2 | tail -1
head -n displays the first n lines of the input
tail -n displays the last n lines of the input
If you really MUST always use the same command, but ensure that the outputs always differ, the only way I can think of to achieve this is using temporary files and a complex sequence of commands:
cat foo.bar.txt.tmp 2>&1 | xargs -I xx echo "| grep -v \\'xx\\' " | tr '\n' ' ' | xargs -I xx sh -c "grep 'foo' bar.txt xx | head -1 | tee -a foo.bar.txt.tmp"
So to explain this command, given foo as a search string and bar.txt as the filename, then foo.bar.txt.tmp is a unique name for a temporary file. The temporary file will hold the strings that have already been output:
cat foo.bar.txt.tmp 2>&1 : outputs the contents of the temporary file. If none is present, will output an error message to stdout, (important because if the output was empty the rest of the command wouldn't work.)
xargs -I xx echo "| grep -v \\'xx\\' " adds | grep -v to the start of each line in the temporary file, grep -v something excludes lines that include something.
tr '\n' ' ' replaces newlines with spaces, to have on a single string a sequence of grep -vs.
xargs -I xx sh -c "grep 'foo' bar.txt xx | head -1 | tee -a foo.bar.txt.tmp" runs a new command, grep 'foo' bar.txt xx | head -1 | tee -a foo.bar.txt.tmp, replacing xx with the previous output. xx should be the sequence of grep -vs that exclude previous outputs.
head -1 makes sure only one line is output at a time
tee -a foo.bar.txt.tmp appends the new output to the temporary file.
Just be sure to clear the temporary files, rm *.tmp, at the end of your script.
If I am getting question right and you want to remove duplicates based on last field of each line then try following(this should be easy task for awk).
awk '!a[$NF]++' Input_file
I have this a file.txt with one line, whose content is
/app/jdk/java/bin/java -server -Xms3g -Xmx3g -XX:MaxPermSize=256m -Dweblogic.Name=O2pPod8_mapp_msrv1_1 -Djava.security.policy=/app/Oracle/Middleware/Oracle_Home/wlserver/server/lib/weblogic.policy -Djava.security.egd=file:/dev/./urandom -Dweblogic.ProductionModeEnabled=true -Dweblogic.system.BootIdentityFile=/app/Oracle/Middleware/Oracle_Home/user_projects/domains/O2pPod8_domain/servers/O2pPod8_mapp_msrv1_1/data/nodemanager/boot.properties -Dweblogic.nodemanager.ServiceEnabled=true -Dweblogic.nmservice.RotationEnabled=true -Dweblogic.security.SSL.ignoreHostnameVerification=false -Dweblogic.ReverseDNSAllowed=false -Xms8192m -Xmx8192m -XX:MaxPermSize=2048m -XX:NewSize=1300m -XX:MaxNewSize=1300m -XX:SurvivorRatio=4 -XX:TargetSurvivorRatio=90 -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:+CMSParallelRemarkEnabled
and when I do
cat file.txt | grep -io "Xms.*" | awk '{FS" "; print $1} ' | cut -d "s" -f2
output:
3g
why is grep not reading the second occurrence, i.e. I expect 3g and 8192m.
Infact, how do I print only 8192m in this case?
Your regex just says "find Xms followed by anything repeated 0 to n times". That returns the rest of the row from Xms onward.
What you actually want is something like "find Xms followed by anything until there's a whitespace repeated 0 to n times".
grep -io "Xms[^ ]*" file.txt | awk '{FS" "; print $1} ' | cut -d "s" -f2
In [^ ] the ^ means "not"
I'm not really sure what you are trying to achieve here but if you want the endings of all space-separated strings starting with -Xms, using bare awk is:
$ awk -v RS=" " '/^-Xms/{print substr($0,5)}' file
3g
8192m
Explained:
$ awk -v RS=" " ' # space separated records
/^-Xms/ { # strings starting with -Xms
print substr($0,5) # print starting from 5th position
}' file
If you wanted something else (word repeated in the title puzzles me a bit), please update the question with more detailed requirements.
Edit: I just noticed how do I print only 8192m in this case (that's the repeated maybe). Let's add a counter c and not print the first instance:
$ awk -v RS=" " '/^-Xms/&&++c>1{print substr($0,5)}' file
8192m
You could use grep -io "Xms[0-9]*[a-zA-Z]" instead of grep -io "Xms.*" to match a sequence of digits followed by a single character instead the entire line within a single group:
cat file.txt | grep -io "Xms[0-9]*[a-zA-Z]" | awk '{FS" "; print $1} ' | cut -d "s" -f2
Hope this helps!
The .* in your regexp is matching the rest of the line, you need [^ ]* instead. Look:
$ grep -o 'Xms.*' file
Xms3g -Xmx3g -XX:MaxPermSize=256m -Dweblogic.Name=O2pPod8_mapp_msrv1_1 -Djava.security.policy=/app/Oracle/Middleware/Oracle_Home/wlserver/server/lib/weblogic.policy -Djava.security.egd=file:/dev/./urandom -Dweblogic.ProductionModeEnabled=true -Dweblogic.system.BootIdentityFile=/app/Oracle/Middleware/Oracle_Home/user_projects/domains/O2pPod8_domain/servers/O2pPod8_mapp_msrv1_1/data/nodemanager/boot.properties -Dweblogic.nodemanager.ServiceEnabled=true -Dweblogic.nmservice.RotationEnabled=true -Dweblogic.security.SSL.ignoreHostnameVerification=false -Dweblogic.ReverseDNSAllowed=false -Xms8192m -Xmx8192m -XX:MaxPermSize=2048m -XX:NewSize=1300m -XX:MaxNewSize=1300m -XX:SurvivorRatio=4 -XX:TargetSurvivorRatio=90 -XX:+UseParNewGC -XX:+UseConcMarkSweepGC -XX:+CMSParallelRemarkEnabled
$ grep -o 'Xms[^ ]*' file
Xms3g
Xms8192m
$ grep -o 'Xms[^ ]*' file | cut -d's' -f2
3g
8192m
$ grep -o 'Xms[^ ]*' file | cut -d's' -f2 | tail -1
8192m
or more concisely:
$ sed 's/.*Xms\([^ ]*\).*/\1/' file
8192m
The positive lookbehind of PCRE (the form: (?<=RE1)RE2) can resolve the problem easily:
$ grep -oP '(?<=Xms)\S+' file.txt
3g
8192m
Explains:
-o: show only the part of a line matching PATTERN.
-P: PATTERN is a Perl regular expression.
(?<=Xms)\S+: matches all continuous non-whitespace strings which are just following the string Xms.
I often have to look for specific strings in a big set of log files with grep. And I get lots of results, on what I must scroll a lot.
Today, the results of grep list the results in alphabetical order. I would like to have my grep results reversed ordered by time, like a ls -ltr would do.
I know I could take the result of ls -ltr and grep file by file. I do it like this:
ls -ltr ${my_log_dir}\* | awk '{print $9}' |xargs grep ${my_pattern}
But I wonder: Is there a simpler way?
PS: I'm using ksh on AIX.
The solution I found (thanks to Fedorqui) was to simply use ls -tr. It assumes the results are passed in the right order through the | to xargs allowing then to do the grep.
My misconception was that since when I us ls, the results arrive not as a single column list but as a multiple column list, it couldn't work as an input for xargs.
Here is the simplest solution to date, since it avoids any awk parsing:
ls -tr ${my_log_dir}\* | xargs grep ${my_pattern}
I checked, and every result of the ls -t are passed to xargs even though they look not as I expected they would enter easily in it:
srv:/papi/tata $ ls -t
addl ieet rrri
ooij lllr sss
srv:/papi/tata $ ls -t |xargs -I{} echo {}
addl
ieet
rrri
ooij
lllr
sss
This will work too use find command:-
find -type f -print0 | xargs -r0 stat -c %y\ %n | sort -r | awk '{print $4}' | sed "s|^\./||"
-print0 in find to preserve files having special characters(whitespaces, tabs)
Print file status (stat with %y (Time of last modification) and %n (%n File name) with output having new-separated (-c)
Reverse sort the output from previous command. (-r for reverse)
awk '{print $4}' printing only the file-name (can be optimized as needed)
Removing the leading ./ from the file-names.
Why does grep -v POLYGON remove many more lines than those matching grep POLYGON?
$ cat BOUNDARIES3D_LV03.nt | grep -v POLYGON | wc
249 782 137001
$ cat BOUNDARIES3D_LV03.nt | grep POLYGON | wc
2441 2753697 51833677
$ cat BOUNDARIES3D_LV03.nt | wc
73078 2975809 91746795
Is this a bug in grep (using: grep (GNU grep) 2.23) or am I misunderstanding something?
Update
It seems that grep aborts at the first matching line containing an invalid character.
The problem was that grep aborts at the first line containing a byte sequence that doesn't evaluate to a character in the current encoding. The following resolved the issue for me:
export LC_ALL="en_US.UTF-8"
I have two files
File1
area a
area b
areaf
File2
area a :aaaa
area b:bbbb
area3:abc
areaf:hsg
area4:uhg
area5:yutr
while read -r line
do
grep -w ^line File2 | cut -d ":" -f2
done < File1
Desired output
aaaa
bbbb
hsg
actual output
grep: can't open a
area a
grep: cant open b
area3:abc
areaf:hsg
area4:uhg
area5:yutr
but when i run grep -w ^"area a" File2 | cut -d ":" -f2 it is giving the correct output :
aaaa
Please assist me on this. i tried for loop also. no success. grep is not working inside loop.
Your variable line might contain "special characters". For example, a space that might be interpreted as a separator by the shell. Or some characters that might be interpreted as pattern metacharacter by grep.
You both need to use fgrep and to quote your variable (I'm not sure -w add anything to that command -- why do you feel the need of it?):
fgrep -w "$line"
But doing so you loose the ability to locate "the first character"
An other option if the "start of line" match is required is to escape the search string:
while read -r line
do
line=$(echo "$line" | sed -e 's/[]\/$*.^|[]/\\&/g')
grep -w "^$line" File2 | cut -d ":" -f2
done < File1
You can achieve the same result without a loop, since grep can read patterns from a file via the -f option. This will be more robust:
grep -f input1 input2 | cut -d: -f2
Gives:
aaaa
bbbb
hsg