File1 contains
hello
hello
I need to write a grep command to print the filename if this file contains more than one "hello". Otherwise, I need grep to exit on failure.
So far I have
grep -c "hello" File1 | grep -v :0
but it outputs
2. How do I get the desired output, which should either be filename File1 or no output at all (from what I understand, no match is a non zero exit code for grep)
with GNU grep for -z:
grep -lz 'hello.*hello' file
e.g.:
$ seq 15 | grep -lz '3.*3'
(standard input)
$ echo $?
0
$ seq 5 | grep -lz '3.*3'
$ echo $?
1
Like this:
#!/bin/bash
count=$(grep -c "hello" "$1")
if ((count > 1)); then
echo "$1"
else
exit 1
fi
Usage:
chmod +x script.sh
./script.sh File1
Explanations:
((...)) is an arithmetic command, which returns an exit status of 0 if the expression is nonzero, or 1 if the expression is zero. Also used as a synonym for "let", if side effects (assignments) are needed. See http://mywiki.wooledge.org/ArithmeticExpression
Using perl in a shell:
perl -0 -le '
my $filename = $ARGV[0];
print $filename if grep { /hello\nhello/ } <>
' file
Related
Why does this command work
echo -ne "\x74\x79\xf4"|grep -aPo "\x74\x79"
and this doesn't?
echo -ne "\x74\x79\xf4"|grep -aPo "\x74\x79\xf4"
The following will work:
echo -ne "\x74\x79\xC3\xB4" | grep -aPo "\x74\x79\xf4"
# ^^^^^^^
echo -ne "\x74\x79\u00F4" | grep -aPo "\x74\x79\xf4"
# ^^^^^^
The \xF4 is not a single byte, it consists of two bytes, C3 and B4. Thus, to encode it properly in the echo command, you need to use \xC3\xB4 sequence.
With \u00F4, you specify the code unit.
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[$NF]++' Input_file
Looking for some help if you will..
I have a virtual machine on RedHat 6.5 with 32gb memory.
A free is showing 24.6gb used, 8.2gb free. Only 418mb is cached, 1.8gb buffers.
Executed a top and sorted by virtual used, and I can only account for about 6gb of that 24.6gb used.
A "ps aux" doesn't show any processes that could be taking the memory.
I am flummoxed and looking for some advice on where I can look to see whats taking the memory?
Any help would be appreciated.
Below Bash Script will help you figure out which application is consuming how much of memory.
#!/bin/bash
# Make sure only root can run our script
if [ "$(id -u)" != "0" ]; then
echo "This script must be run as root" 1>&2
exit 1
fi
### Functions
#This function will count memory statistic for passed PID
get_process_mem ()
{
PID=$1
#we need to check if 2 files exist
if [ -f /proc/$PID/status ];
then
if [ -f /proc/$PID/smaps ];
then
#here we count memory usage, Pss, Private and Shared = Pss-Private
Pss=`cat /proc/$PID/smaps | grep -e "^Pss:" | awk '{print $2}'| paste -sd+ | bc `
Private=`cat /proc/$PID/smaps | grep -e "^Private" | awk '{print $2}'| paste -sd+ | bc `
#we need to be sure that we count Pss and Private memory, to avoid errors
if [ x"$Rss" != "x" -o x"$Private" != "x" ];
then
let Shared=${Pss}-${Private}
Name=`cat /proc/$PID/status | grep -e "^Name:" |cut -d':' -f2`
#we keep all results in bytes
let Shared=${Shared}*1024
let Private=${Private}*1024
let Sum=${Shared}+${Private}
echo -e "$Private + $Shared = $Sum \t $Name"
fi
fi
fi
}
#this function make conversion from bytes to Kb or Mb or Gb
convert()
{
value=$1
power=0
#if value 0, we make it like 0.00
if [ "$value" = "0" ];
then
value="0.00"
fi
#We make conversion till value bigger than 1024, and if yes we divide by 1024
while [ $(echo "${value} > 1024"|bc) -eq 1 ]
do
value=$(echo "scale=2;${value}/1024" |bc)
let power=$power+1
done
#this part get b,kb,mb or gb according to number of divisions
case $power in
0) reg=b;;
1) reg=kb;;
2) reg=mb;;
3) reg=gb;;
esac
echo -n "${value} ${reg} "
}
#to ensure that temp files not exist
[[ -f /tmp/res ]] && rm -f /tmp/res
[[ -f /tmp/res2 ]] && rm -f /tmp/res2
[[ -f /tmp/res3 ]] && rm -f /tmp/res3
#if argument passed script will show statistic only for that pid, of not – we list all processes in /proc/ #and get statistic for all of them, all result we store in file /tmp/res
if [ $# -eq 0 ]
then
pids=`ls /proc | grep -e [0-9] | grep -v [A-Za-z] `
for i in $pids
do
get_process_mem $i >> /tmp/res
done
else
get_process_mem $1>> /tmp/res
fi
#This will sort result by memory usage
cat /tmp/res | sort -gr -k 5 > /tmp/res2
#this part will get uniq names from process list, and we will add all lines with same process list
#we will count nomber of processes with same name, so if more that 1 process where will be
# process(2) in output
for Name in `cat /tmp/res2 | awk '{print $6}' | sort | uniq`
do
count=`cat /tmp/res2 | awk -v src=$Name '{if ($6==src) {print $6}}'|wc -l| awk '{print $1}'`
if [ $count = "1" ];
then
count=""
else
count="(${count})"
fi
VmSizeKB=`cat /tmp/res2 | awk -v src=$Name '{if ($6==src) {print $1}}' | paste -sd+ | bc`
VmRssKB=`cat /tmp/res2 | awk -v src=$Name '{if ($6==src) {print $3}}' | paste -sd+ | bc`
total=`cat /tmp/res2 | awk '{print $5}' | paste -sd+ | bc`
Sum=`echo "${VmRssKB}+${VmSizeKB}"|bc`
#all result stored in /tmp/res3 file
echo -e "$VmSizeKB + $VmRssKB = $Sum \t ${Name}${count}" >>/tmp/res3
done
#this make sort once more.
cat /tmp/res3 | sort -gr -k 5 | uniq > /tmp/res
#now we print result , first header
echo -e "Private \t + \t Shared \t = \t RAM used \t Program"
#after we read line by line of temp file
while read line
do
echo $line | while read a b c d e f
do
#we print all processes if Ram used if not 0
if [ $e != "0" ]; then
#here we use function that make conversion
echo -en "`convert $a` \t $b \t `convert $c` \t $d \t `convert $e` \t $f"
echo ""
fi
done
done < /tmp/res #this part print footer, with counted Ram usage echo "--------------------------------------------------------" echo -e "\t\t\t\t\t\t `convert $total`" echo "========================================================" # we clean temporary file [[ -f /tmp/res ]] && rm -f /tmp/res [[ -f /tmp/res2 ]] && rm -f /tmp/res2 [[ -f /tmp/res3 ]] && rm -f /tmp/res3
I am going to take a wild stab at this. Without having access to the machine or additional information troubleshooting this will be difficult.
The /tmp file system is special in that it exists entirely in memory. There are a couple others that are like this but /tmp is a special flower. Check the disk usage on this directory and you may see where your memory is getting consumed. ( du -sh /tmp )
1st issue : My code is working only if grep take constant pattern like this :
echo "$s" | grep -oP '(?<=class="A3">).*(?=</a>)'
2nd issue : assigning output to a variable not working too
Here is my script :
#!/bin/sh
filename="data.txt"
Ptr_ValidChannel="><a title=\"Id: "
Ptr_ChannelNameStart="<class=\"A3\">"
Ptr_ChannelNameEnd="</a>"
while read -r line
do
case "$line" in
# working 100%
#*$Ptr_ValidChannel*) echo "$line" | grep -oP '(?<=class="A3">).*?(?=</a>)' ;;
# not working
#*$Ptr_ValidChannel*) echo $line | grep -oP '(?<=$Ptr_ChannelNameStart).*?(?=$Ptr_ChannelNameEnd)' ;;
# not working
*$Ptr_ValidChannel*) myvar=$(echo $line | grep -oP '(?<=$Ptr_ChannelNameStart).*?(?=$Ptr_ChannelNameEnd)') ;;
esac
done < "$filename"
echo $var_name
exit
To simplify things the data.txt content is :
<TD WIDTH="15%"><a title="Id: I24 NEWS" class="A3">I24 News Français</a><br /><font color="#555555"> <a title="Sporadic or full 16/9 transmission"><img src="/169.gif"></a>
In my system the command :
ls -la /bin/sh
output is :
/bin/sh -> dash
best regards.
PS. NO BASH CODE PLEASE. ONLY SH.
After reading this article: dash as bin sh. i figured out what to do to make my code work correctly and more portable:
#! /bin/sh
filename='data.txt'
Ptr_ValidChannel='><a title="Id: '
Ptr_ChannelNameStart='class="A3">'
Ptr_ChannelNameEnd='</a>'
while read -r line
do
case "$line" in
*"$Ptr_ValidChannel"*) var_name=$(printf %s "$line" | grep -oP '(?<='"$Ptr_ChannelNameStart"').*?(?='"$Ptr_ChannelNameEnd"')'); printf %s "$var_name"; printf '\n'; ;;
esac
done < "$filename"
exit
Thank you for your comments
best reagrds.
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