I have a file of strings that I need to search for in another file. So I've tried the following code:
#!/bin/bash
while read name; do
#echo $name
grep "$name" file.txt > results.txt
done < missing.txt
The echo line confirms the file is being read into the variable, but my results file is always empty. Doing the grep command on its own works, I'm obviously missing something very basic here but I have been stuck for a while and can't figure it out.
I've also tried without quotes around the variable. Can someone tell me what I'm missing? Thanks a bunch
Edit - input file was DOS format, set file format to unix and works fine now
Use grep's -f option: Then you only need a single grep call and no loop.
grep -f missing.txt file.txt > results.txt
If the contents of "missing.txt" are fixed strings, not regular expressions, this will speed up the process:
grep -F -f missing.txt file.txt > results.txt
And if you want to find the words of missing.txt in the other file, not partial words
grep -F -w -f missing.txt file.txt > results.txt
My first guess is that you are overwriting your results.txt file in every iteration of the while loop (with the single >). If it is the case you should at least have the result for the very last line in your missing.txt file. Then I think it would suffice to do something like
#!/bin/bash
while read name; do
#echo "$name"
grep "$name" file.txt
done < missing.txt > results.txt
Related
I have these files
NotRequired.txt (having lines which need to be remove)
Need2CleanSED.txt (big file , need to clean)
Need2CleanGRP.txt (big file , need to clean)
content:
more NotRequired.txt
[abc-xyz_pqr-pe2_123]
[lon-abc-tkt_1202]
[wat-7600-1_414]
[indo-pak_isu-5_761]
I am reading above file and want to remove lines from Need2Clean???.txt, trying via SED and GREP but no success.
myFile="NotRequired.txt"
while IFS= read -r HKline
do
sed -i '/$HKline/d' Need2CleanSED.txt
done < "$myFile"
myFile="NotRequired.txt"
while IFS= read -r HKline
do
grep -vE \"$HKline\" Need2CleanGRP.txt > Need2CleanGRP.txt
done < "$myFile"
Looks as if the Variable and characters [] making some problem.
What you're doing is extremely inefficient and error prone. Just do this:
grep -vF -f NotRequired.txt Need2CleanGRP.txt > tmp &&
mv tmp Need2CleanGRP.txt
Thanks to grep -F the above treats each line of NotRequired.txt as a string rather than a regexp so you don't have to worry about escaping RE metachars like [ and you don't need to wrap it in a shell loop - that one command will remove all undesirable lines in one execution of grep.
Never do command file > file btw as the shell might decide to execute the > file first and so empty file before command gets a chance to read it! Always do command file > tmp && mv tmp file instead.
Your assumption is correct. The [...] construct looks for any characters in that set, so you have to preface ("escape") them with \. The easiest way is to do that in your original file:
sed -i -e 's:\[:\\[:' -e 's:\]:\\]:' "${myFile}"
If you don't like that, you can probably put the sed command in where you're directing the file in:
done < replace.txt|sed -e 's:\[:\\[:' -e 's:\]:\\]:'
Finally, you can use sed on each HKline variable:
HKline=$( echo $HKline | sed -e 's:\[:\\[:' -e 's:\]:\\]:' )
try gnu sed:
sed -Ez 's/\n/\|/g;s!\[!\\[!g;s!\]!\\]!g; s!(.*).!/\1/d!' NotRequired.txt| sed -Ef - Need2CleanSED.txt
Two sed process are chained into one by shell pipe
NotRequired.txt is 'slurped' by sed -z all at once and substituted its \n and [ meta-char with | and \[ respectively of which the 2nd process uses it as regex script for the input file, ie. Need2CleanSED.txt. 1st process output;
/\[abc-xyz_pqr-pe2_123\]|\[lon-abc-tkt_1202\]|\[wat-7600-1_414\]|\[indo-pak_isu-5_761\]/d
add -u ie. unbuffered, option to evade from batch process, sort of direct i/o
I have some files in fasta format and want to counts their reads and would like to have output in file names and their corresponding counts.
input file names:
1.fa
2.fa
3.fa
...
I tried:
for i in $(ls -t -v *.fa); do grep -c '>' $i > echo $i >> out.txt ; done
Problem:
It gives me out.txt but double file names and their counts by ':' separated. However, I need a tab and unique file names.
1.fa:7323580
1.fa:7323580
2.fa:5591179
2.fa:5591179
...
Suggested solution
grep -c '>' *.fa | sed 's/:/'$'\t'/ > out.txt
The $'\t\' is a Bash-ism called ANSI C Quoting.
Analysis of what went wrong
Your code is:
for i in $(ls -t -v *.fa); do grep -c '>' $i > echo $i >> out.txt ; done
It isn't a good idea to parse the output of the ls command. However, if your file names are well behaved (roughly, in the portable filename character set, which is [-A-Za-z._]), you'll be reasonably OK.
Your grep command, though, is confused. It is:
grep -c '>' $i > echo $i >> out.txt
That could be written more clearly as:
grep -c '>' $i $i > echo >> out.txt
This means 'count the number of lines containing > in $i, and then in $i again, and send the output first to a file echo, and then append to out.txt. Since the append overrides the redirection, the file echo is empty. You get the file name included in the output because there are two files to search; with only one file, you wouldn't get the file name too. (One way to ensure you get file names with regular (not -c or -l) grep is to scan /dev/null too. Many versions of grep also provide options to get the name explicitly, but POSIX doesn't mandate one. BSD grep uses -H; so does GNU grep.)
So, that's why you got the double file names and entries in your output.
Try this:
for i in $(ls -t -v *.fa)
do
c=$(grep -c '>' $i | awk -F: '{print $2}')
echo "$i: $c" >> out.txt
done
I have hundreds of text files in one directory. For all files, I want to delete all the lines that begin with HETATM. I would need a csh or bash code.
I would think you would use grep, but I'm not sure.
Use sed like this:
sed -i -e '/^HETATM/d' *.txt
to process all files in place.
-i means "in place".
-e means to execute the command that follows.
/^HETATM/ means "find lines starting with HETATM", and the following d means "delete".
Make a backup first!
If you really want to do it with grep, you could do this:
#!/bin/bash
for f in *.txt
do
grep -v "^HETATM" "%f" > $$.tmp && mv $$.tmp "$f"
done
It makes a temporary file of the output from grep (in file $$.tmp) and only overwrites your original file if the command executes successfully.
Using the -v option of grep to get all the lines that do not match:
grep -v '^HETATM' input.txt > output.txt
I have a list of files (~1000) and there is 1 file per line in my text file named: 'files.txt'
I have a macro that looks something like the following:
#!/bin/sh
b=$(sed '${1}q;d' files.txt)
cat > MyMacro_${1}.C << +EOF
myFile = new TFile("/MYPATHNAME/$b");
+EOF
and I use this input script by doing
./MakeMacro.sh 1
and later I want to do
./MakeMacro.sh 2
./MakeMacro.sh 3
...etc
So that it reads the n'th line of my files.txt and feeds that string to my created .C macro.
So that it reads the n'th line of my files.txt and feeds that string to my created .C macro.
Given this statement and your tags, I'm going to answer using shell tools and not really address the issue of the .c macro.
The first line of your script contains a sed script. There are numerous ways to get the Nth line from a text file. The simplest might be to use head and tail.
$ head -n "${i}" files.txt | tail -n 1
This takes the first $i lines of files.txt, and shows you the last 1 lines of that set.
$ sed -ne "${i}p" files.txt
This use of sed uses -n to avoid printing by default, then prints the $ith line. For better performance, try:
$ sed -ne "${i}{p;q;}" files.txt
This does the same, but quits after printing the line, so that sed doesn't bother traversing the rest of the file.
$ awk -v i="$i" 'NR==i' files.txt
This passes the shell variable $i into awk, then evaluates an expression that tests whether the number of records processed is the same as that variable. If the expression evaluates true, awk prints the line. For better performance, try:
$ awk -v i="$i" 'NR==i{print;exit}' files.txt
Like the second sed script above, this will quit after printing the line, so as to avoid traversing the rest of the file.
Plenty of ways you could do this by loading the file into an array as well, but those ways would take more memory and perform less well. I'd use one-liners if you can. :)
To take any of these one-liners and put it into your script, you already have the notation:
if expr "$i" : '[0-9][0-9]*$' >/dev/null; then
b=$(sed -ne "${i}{p;q;}" files.txt)
else
echo "ERROR: invalid line number" >&2; exit 1
fi
If I am understanding you correctly, you can do a for loop in bash to call the script multiple times with different arguments.
for i in `seq 1 n`; do ./MakeMacro.sh $i; done
Based on the OP's comment, it seems that he wants to submit the generated files to Condor. You can modify the loop above to include the condor submission.
for i in `seq 1 n`; do ./MakeMacro.sh $i; condor_submit <OutputFile> ; done
i=0
while read file
do
((i++))
cat > MyMacro_${i}.C <<-'EOF'
myFile = new TFile("$file");
EOF
done < files.txt
Beware: you need tab indents on the EOF line.
I'm puzzled about why this is the way you want to do the job. You could have your C++ code read files.txt at runtime and it would likely be more efficient in most ways.
If you want to get the Nth line of files.txt into MyMacro_N.C, then:
{
echo
sed -n -e "${1}{s/.*/myFile = new TFILE(\"&\");/p;q;}" files.txt
echo
} > MyMacro_${1}.C
Good grief. The entire script should just be (untested):
awk -v nr="$1" 'NR==nr{printf "\nmyFile = new TFile(\"/MYPATHNAME/%s\");\n\n",$0 > ("MyMacro_"nr".C")}' files.txt
You can throw in a ;exit before the } if performance is an issue but I doubt if it will be.
I am trying to modify a bash script to remove a glob of malicious code from a large number of files.
The community will benefit from this, so here it is:
#!/bin/bash
grep -r -l 'var createDocumentFragm' /home/user/Desktop/infected_site/* > /home/user/Desktop/filelist.txt
for i in $(cat /home/user/Desktop/filelist.txt)
do
cp -f $i $i.bak
done
for i in $(cat /home/user/Desktop/filelist.txt)
do
$i | sed 's/createDocumentFragm.*//g' > $i.awk
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
This is where the script bombs out with this message:
+ for i in '$(cat /home/user/Desktop/filelist.txt)'
+ sed 's/createDocumentFragm.*//g'
+ /home/user/Desktop/infected_site/index.htm
I get 2 errors and the script stops.
/home/user/Desktop/infected_site/index.htm: line 1: syntax error near unexpected token `<'
/home/user/Desktop/infected_site/index.htm: line 1: `<html><head><script>(function (){ '
I have the first 2 parts done.
The files containing createDocumentfragm have been enumerated in a text file correctly.
The files in the textfile.txt have been duplicated, in their original location with a .bak added to them IE: infected_site/some_directory/infected_file.htm and infected_file.htm.bak
effectively making sure we have a backup.
All I need to do now is write an AWK command that will use the list of files in filelist.txt, use the entire glob of malicious text as a pattern, and remove it from the files. Using just the uppercase script as the starting point, and the lower case script is too generic and could delete legitimate text
I suspect this may help me, but I don't know how to use it correctly.
http://backreference.org/2010/03/13/safely-escape-variables-in-awk/
Once I have this part figured out, and after you have verified that the files weren't mangled you can do this to clean out the bak files:
for i in $(cat /home/user/Desktop/filelist.txt)
do
rm -f $i.bak
done
Several things:
You have:
$i | sed 's/var createDocumentFragm.*//g' > $i.awk
You should probably meant this (using your use of cat which we'll talk about in a moment):
cat $i | sed 's/var createDocumentFragm.*//g' > $i.awk
You're treating each file in your file list as if it was a command and not a file.
Now, about your use of cat. If you're using cat for almost anything but concatenating multiple files together, you probably are doing something not quite right. For example, you could have done this:
sed 's/var createDocumentFragm.*//g' "$i" > $i.awk
I'm also a bit confused about the awk statement. Exactly what file are you using awk on? Your awk statement is using STDIN and STDOUT, so it's reading file names from the for loop and then printing the output on the screen. Is the sed statement suppose to feed into the awk statement?
Note that I don't have to print out my file to STDOUT, then pipe that into sed. The sed command can take the file name directly.
You also want to avoid for loops over a list of files. That is very inefficient, and can cause problems with the command line getting overloaded. Not a big issue today, but can affect you when you least suspect it. What happens is that your $(cat /home/user/Desktop/filelist.txt) must execute first before the for loop can even start.
A little rewriting of your program:
cd ~/Desktop
grep -r -l 'var createDocumentFragm' infected_site/* > filelist.txt
while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
We can use one loop, and we made it a while loop. I could even feed the grep into that while loop:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" > "$i.awk"
awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p'
done < filelist.txt
and then I don't even have to create a temporary file.
Let me know what's going on with the awk. I suspect you wanted something like this:
grep -r -l 'var createDocumentFragm' infected_site/* | while read file
do
cp -f "$file" "$file.bak"
sed 's/var createDocumentFragm.*//g' "$file" \
| awk '/<\/SCRIPT>/{p=1;print}/<\/script>/{p=0}!p' > "$i.awk"
done < filelist.txt
Also note I put quotes around file names. This helps prevent problems if file name has a space in it.