I'm trying to grep a non-literal such as "." So I found a similar question Grep single quote and dollar sign
But I'm stuck on resolve to grep such as "." in shell as below.
#!/bin/csh
if ($#argv != 2) then
echo "you must give exactly two parameters"
else
echo "$argv[1]" "$argv[2]"
find -name "$argv[1]" | xargs grep -n "$argv[2]"
endif
I try it with 2 arguments
$> "*.dat" "this."
but grep does not exactly work what I expect "this." grep only report to "this" without "."
Related
Team,
I want to grep for a substring container - and then only output that string and not whole line. how can i? I know i can awk on space and pull using $ but want to know how to do in grep?
echo $test_pods_info | grep -F 'test-'
output
test-78ac951e-89a6-4199-87a4-db8a1b8b054f export-9b55f0d5-071d-431-1d2ux0-avexport-xavierisp-sjc4--a4dd85-102 1/1 Running 0 19h
expected output
test-78ac951e-89a6-4199-87a4-db8a1b8b054f
awk is more suitable for this as you want to get first field in a matching line:
awk '/test-/{print $1}' <<< "$taxIncluded"
test-78ac951e-89a6-4199-87a4-db8a1b8b054f
If you really want to use grep then this might be what you're looking for:
grep -o 'test-\S*' <<< "$taxIncluded"
or:
grep -o 'test-[^[:space:]]*' <<< "$taxIncluded"
Try
echo $test_pods_info | grep -o 'test-'
the -o option is:
show[ing] only the part of a line matching PATTERN
according to grep --help. Of course, this will only print test-, so you'll need to rework your regex:
grep -oE '(test).*[[:space:]]\b'
Figured it out..
echo $test_pods_info | grep -o "\test-\w*-\w*\-\w*\-\w*\-\w*"
outoput
test-78ac951e-89a6-4199-87a4-db8a1b8b054f
but i wish there is simple way. like \test-*\
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
After reading the xargs man page, I am unable to understand the difference in exit codes from the following xargs invocations.
(The original purpose was to combine find and grep to check if an expressions exists in ALL the given files when I came across this behaviour)
To reproduce:
(use >>! if using zsh to force creation of file)
# Create the input files.
echo "a" >> 1.txt
echo "ab" >> 2.txt
# The end goal is to check for a pattern (in this case simply 'b') inside
# ALL the files returned by a find search.
find . -name "1.txt" -o -name "2.txt" | xargs -I {} grep -q "b" {}
echo $?
123 # Works as expected since 'b' is not present in 1.txt
find . -name "1.txt" -o -name "2.txt" | xargs grep -q "b"
echo $?
0 # Am more puzzled by why the behaviour is inconsistent
The EXIT_STATUS section on the man page says:
xargs exits with the following status:
0 if it succeeds
123 if any invocation of the command exited with status 1-125
124 if the command exited with status 255
125 if the command is killed by a signal
126 if the command cannot be run
127 if the command is not found
1 if some other error occurred.
I would have thought, that 123 if any invocation of the command exited with status 1-125 should apply irrespective of whether or not -I is used ?
Could you share any insights to explain this conundrum please?
Here is evidence of the effect of -I option with xargs with the help of a wrapper script which shows the number of invocations:
cat ./grep.sh
#/bin/bash
echo "I am being invoked at $(date +%Y%m%d_%H-%M-%S)"
grep $#
(the actual command being invoked, in this case grep doesn't really matter)
Now execute the same commands as in the question using the wrapper script instead:
❯ find . -name "1.txt" -o -name "2.txt" | xargs -I {} ./grep.sh -q "b" {}
I am being invoked at 20190410_09-46-29
I am being invoked at 20190410_09-46-30
❯ find . -name "1.txt" -o -name "2.txt" | xargs ./grep.sh -q "b"
I am being invoked at 20190410_09-46-53
I have just discovered a comment on the answer of a similar question that answers this question (complete credit to https://superuser.com/users/49184/daniel-andersson for his wisdom):
https://superuser.com/questions/557203/xargs-i-behaviour#comment678705_557230
Also, unquoted blanks do not terminate input items; instead the separator is the newline character. — this is central to understanding the behavior. Without -I, xargs only sees the input as a single field, since newline is not a field separator. With -I, suddenly newline is a field separator, and thus xargs sees three fields (that it iterates over). That is a real subtle point, but is explained in the man page quoted.
-I replace-str
Replace occurrences of replace-str in the initial-arguments
with names read from standard input. Also, unquoted blanks do
not terminate input items; instead the separator is the
newline character. Implies -x and -L 1.
Based on that,
find . -name "1.txt" -o -name "2.txt"
#returns
# ./1.txt
# ./2.txt
xargs -I {} grep -q "b" {}
# interprets the above as two separate lines since,
# with -I option the newline is now a *field separator*.
# So this results in TWO invocations of grep and since one of them fails,
# the overall output is 123 as documented in the EXIT_STATUS section
xargs grep -q "b"
# interprets the above as a single input field,
# so a single grep invocation which returns a successful exit code of 0 since the pattern was found in one of the files.
I'm trying to grep for a string that starts with "--"
for some reason it counted as special character, but even when trying to use -F then grep gives me bad syntax:
[root#pc-01 /]# grep -F --restore .
-bash: --restore: command not found
any tips?
Thanks.
Try following.
grep -F -- --restore filename
You can escape the first - :
Without escaping:
[root#TIAGO-TEST2 tmp]# echo '--aa --bb --cc' | grep -o '--b'
grep: option '--b' is ambiguous; possibilities: '--basic-regexp' '--binary' '--byte-offset' '--binary-files' '--before-context'
Usage: grep [OPTION]... PATTERN [FILE]...
Try `grep --help' for more information.
Escaping:
[root#TIAGO-TEST2 tmp]# echo '--aa --bb --cc' | grep -o '\--b'
--b
I'm trying to grep multiple extensions within the current and all sub-folders.
grep -i -r -n 'hello' somepath/*.{php,html}
This is only grepping the current folder but not sub-folders.
What would be a good way of doing this?
Using only grep:
grep -irn --include='*.php' --include='*.html' 'hello' somepath/
One of these:
find '(' -name '*.php' -o -name '*.html' ')' -exec grep -i -n hello {} +
find '(' -name '*.php' -o -name '*.html' ')' -print0 | xargs -0 grep -i -n hello
I was looking the same and when decided to do a bash script I started with vim codesearch and surprise I already did this before!
#!/bin/bash
context="$3"
#ln = line number mt = match mc = file
export GREP_COLORS="sl=32:mc=00;33:ms=05;40;31:ln="
if [[ "$context" == "" ]]; then context=5; fi
grep --color=always -n -a -R -i -C"$context" --exclude='*.mp*'\
--exclude='*.avi'\
--exclude='*.flv'\
--exclude='*.png'\
--exclude='*.gif'\
--exclude='*.jpg'\
--exclude='*.wav'\
--exclude='*.rar'\
--exclude='*.zip'\
--exclude='*.gz'\
--exclude='*.sql' "$2" "$1" | less -R
paste this code into in a file named codesearch and set the chmod to 700 or 770
I guess this could be better here for the next time that I forgot
this script will show with colors the matches and the context around
./codesearch '/full/path' 'string to search'
and optional defining the number of context line around default 5
./codesearch '/full/path' 'string to search' 3
I edited the code and added some eye candy
example ./codesearch ./ 'eval' 2
Looks like this when you have enabled "allow blinking text" in terminal