I am trying to remove 500+ non-consecutive lines from a very large file with sed.
I have the lines stored in a list.txt file but I cant't use it in a for loop
for i in `cat list`; do echo 'sed -i -e ' \'"$i"d\'' huge_file.txt' ; done
because line numbers in the original file would change every time sed removes one and exits.
I should do:
sed -i -e '1d;2d;93572277d;93572278d; ......;nth ' huge_file.txt
Is there a way to pass that list to sed in a file?
you can try with awk:
awk -v s="2,3,..,n" 'BEGIN{n=split(s,t,",");for(i=1;i<=n;i++)d[t[i]]=1}
!d[NR]' huge.txt
You pass the comma-separated line numbers to awk by -v, in awk split it in array, and check each line, if the line number in the array, skip.
Test it with small file, if it worked as you expected, you can do:
awk -v '....' '....' huge.txt > tmp.txt && mv tmp.txt huge.txt
to write the change back to your original input file.
update
If you have 500 line numbers in another file, say, each number in a line, you can:
awk 'NR==FNR{a[$0]=1;next}!a[FNR]' ln.txt huge.txt
If it's just for a single particular task (not frequent) you may use the following GNU sed approach (assuming that numbers in list.txt are separated with newline \n):
sed -i "$(sed -z 's/\n/d;/g' list.txt)" huge_file.txt
Related
I am interested in concatenate many files together based on the numeric number and also remove the first line.
e.g. chr1_smallfiles then chr2_smallfiles then chr3_smallfiles.... etc (each without the header)
Note that chr10_smallfiles needs to come after chr9_smallfiles -- that is, this needs to be numeric sort order.
When separate the two command awk and ls -v1, each does the job properly, but when put them together, it doesn't work. Please help thanks!
awk 'FNR>1' | ls -v1 chr*_smallfiles > bigfile
The issue is with the way that you're trying to pass the list of files to awk. At the moment, you're piping the output of awk to ls, which makes no sense.
Bear in mind that, as mentioned in the comments, ls is a tool for interactive use, and in general its output shouldn't be parsed.
If sorting weren't an issue, you could just use:
awk 'FNR > 1' chr*_smallfiles > bigfile
The shell will expand the glob chr*_smallfiles into a list of files, which are passed as arguments to awk. For each filename argument, all but the first line will be printed.
Since you want to sort the files, things aren't quite so simple. If you're sure the full range of files exist, just replace chr*_smallfiles with chr{1..99}_smallfiles in the original command.
Using some Bash-specific and GNU sort features, you can also achieve the sorting like this:
printf '%s\0' chr*_smallfiles | sort -z -n -k1.4 | xargs -0 awk 'FNR > 1' > bigfile
printf '%s\0' prints each filename followed by a null-byte
sort -z sorts records separated by null-bytes
-n -k1.4 does a numeric sort, starting from the 4th character (the numeric part of the filename)
xargs -0 passes the sorted, null-separated output as arguments to awk
Otherwise, if you want to go through the files in numerical order, and you're not sure whether all the files exist, then you can use a shell loop (although it'll be significantly slower than a single awk invocation):
for file in chr{1..99}_smallfiles; do # 99 is the maximum file number
[ -f "$file" ] || continue # skip missing files
awk 'FNR > 1' "$file"
done > bigfile
You can also use tail to concatenate all the files without header
tail -q -n+2 chr*_smallfiles > bigfile
In case you want to concatenate the files in a natural sort order as described in your quesition, you can pipe the result of ls -v1 to xargs using
ls -v1 chr*_smallfiles | xargs -d $'\n' tail -q -n+2 > bigfile
(Thanks to Charles Duffy) xargs -d $'\n' sets the delimiter to a newline \n in case the filename contains white spaces or quote characters
Using a bash 4 associative array to extract only the numeric substring of each filename; sort those individually; and then retrieve and concatenate the full names in the resulting order:
#!/usr/bin/env bash
case $BASH_VERSION in ''|[123].*) echo "Requires bash 4.0 or newer" >&2; exit 1;; esac
# when this is done, you'll have something like:
# files=( [1]=chr_smallfiles1.txt
# [10]=chr_smallfiles10.txt
# [9]=chr_smallfiles9.txt )
declare -A files=( )
for f in chr*_smallfiles.txt; do
files[${f//[![:digit:]]/}]=$f
done
# now, emit those indexes (1, 10, 9) to "sort -n -z" to sort them as numbers
# then read those numbers, look up the filenames associated, and pass to awk.
while read -r -d '' key; do
awk 'FNR > 1' <"${files[$key]}"
done < <(printf '%s\0' "${!files[#]}" | sort -n -z) >bigfile
You can do with a for loop like below, which is working for me:-
for file in chr*_smallfiles
do
tail +2 "$file" >> bigfile
done
How will it work? For loop read all the files from current directory with wild chard character * chr*_smallfiles and assign the file name to variable file and tail +2 $file will output all the lines of that file except the first line and append in file bigfile. So finally all files will be merged (accept the first line of each file) into one i.e. file bigfile.
Just for completeness, how about a sed solution?
for file in chr*_smallfiles
do
sed -n '2,$p' $file >> bigfile
done
Hope it helps!
How would I use sed to delete all lines in a text file that contain a specific string?
To remove the line and print the output to standard out:
sed '/pattern to match/d' ./infile
To directly modify the file – does not work with BSD sed:
sed -i '/pattern to match/d' ./infile
Same, but for BSD sed (Mac OS X and FreeBSD) – does not work with GNU sed:
sed -i '' '/pattern to match/d' ./infile
To directly modify the file (and create a backup) – works with BSD and GNU sed:
sed -i.bak '/pattern to match/d' ./infile
There are many other ways to delete lines with specific string besides sed:
AWK
awk '!/pattern/' file > temp && mv temp file
Ruby (1.9+)
ruby -i.bak -ne 'print if not /test/' file
Perl
perl -ni.bak -e "print unless /pattern/" file
Shell (bash 3.2 and later)
while read -r line
do
[[ ! $line =~ pattern ]] && echo "$line"
done <file > o
mv o file
GNU grep
grep -v "pattern" file > temp && mv temp file
And of course sed (printing the inverse is faster than actual deletion):
sed -n '/pattern/!p' file
You can use sed to replace lines in place in a file. However, it seems to be much slower than using grep for the inverse into a second file and then moving the second file over the original.
e.g.
sed -i '/pattern/d' filename
or
grep -v "pattern" filename > filename2; mv filename2 filename
The first command takes 3 times longer on my machine anyway.
The easy way to do it, with GNU sed:
sed --in-place '/some string here/d' yourfile
You may consider using ex (which is a standard Unix command-based editor):
ex +g/match/d -cwq file
where:
+ executes given Ex command (man ex), same as -c which executes wq (write and quit)
g/match/d - Ex command to delete lines with given match, see: Power of g
The above example is a POSIX-compliant method for in-place editing a file as per this post at Unix.SE and POSIX specifications for ex.
The difference with sed is that:
sed is a Stream EDitor, not a file editor.BashFAQ
Unless you enjoy unportable code, I/O overhead and some other bad side effects. So basically some parameters (such as in-place/-i) are non-standard FreeBSD extensions and may not be available on other operating systems.
I was struggling with this on Mac. Plus, I needed to do it using variable replacement.
So I used:
sed -i '' "/$pattern/d" $file
where $file is the file where deletion is needed and $pattern is the pattern to be matched for deletion.
I picked the '' from this comment.
The thing to note here is use of double quotes in "/$pattern/d". Variable won't work when we use single quotes.
You can also use this:
grep -v 'pattern' filename
Here -v will print only other than your pattern (that means invert match).
To get a inplace like result with grep you can do this:
echo "$(grep -v "pattern" filename)" >filename
I have made a small benchmark with a file which contains approximately 345 000 lines. The way with grep seems to be around 15 times faster than the sed method in this case.
I have tried both with and without the setting LC_ALL=C, it does not seem change the timings significantly. The search string (CDGA_00004.pdbqt.gz.tar) is somewhere in the middle of the file.
Here are the commands and the timings:
time sed -i "/CDGA_00004.pdbqt.gz.tar/d" /tmp/input.txt
real 0m0.711s
user 0m0.179s
sys 0m0.530s
time perl -ni -e 'print unless /CDGA_00004.pdbqt.gz.tar/' /tmp/input.txt
real 0m0.105s
user 0m0.088s
sys 0m0.016s
time (grep -v CDGA_00004.pdbqt.gz.tar /tmp/input.txt > /tmp/input.tmp; mv /tmp/input.tmp /tmp/input.txt )
real 0m0.046s
user 0m0.014s
sys 0m0.019s
Delete lines from all files that match the match
grep -rl 'text_to_search' . | xargs sed -i '/text_to_search/d'
SED:
'/James\|John/d'
-n '/James\|John/!p'
AWK:
'!/James|John/'
/James|John/ {next;} {print}
GREP:
-v 'James\|John'
perl -i -nle'/regexp/||print' file1 file2 file3
perl -i.bk -nle'/regexp/||print' file1 file2 file3
The first command edits the file(s) inplace (-i).
The second command does the same thing but keeps a copy or backup of the original file(s) by adding .bk to the file names (.bk can be changed to anything).
You can also delete a range of lines in a file.
For example to delete stored procedures in a SQL file.
sed '/CREATE PROCEDURE.*/,/END ;/d' sqllines.sql
This will remove all lines between CREATE PROCEDURE and END ;.
I have cleaned up many sql files withe this sed command.
echo -e "/thing_to_delete\ndd\033:x\n" | vim file_to_edit.txt
Just in case someone wants to do it for exact matches of strings, you can use the -w flag in grep - w for whole. That is, for example if you want to delete the lines that have number 11, but keep the lines with number 111:
-bash-4.1$ head file
1
11
111
-bash-4.1$ grep -v "11" file
1
-bash-4.1$ grep -w -v "11" file
1
111
It also works with the -f flag if you want to exclude several exact patterns at once. If "blacklist" is a file with several patterns on each line that you want to delete from "file":
grep -w -v -f blacklist file
to show the treated text in console
cat filename | sed '/text to remove/d'
to save treated text into a file
cat filename | sed '/text to remove/d' > newfile
to append treated text info an existing file
cat filename | sed '/text to remove/d' >> newfile
to treat already treated text, in this case remove more lines of what has been removed
cat filename | sed '/text to remove/d' | sed '/remove this too/d' | more
the | more will show text in chunks of one page at a time.
Curiously enough, the accepted answer does not actually answer the question directly. The question asks about using sed to replace a string, but the answer seems to presuppose knowledge of how to convert an arbitrary string into a regex.
Many programming language libraries have a function to perform such a transformation, e.g.
python: re.escape(STRING)
ruby: Regexp.escape(STRING)
java: Pattern.quote(STRING)
But how to do it on the command line?
Since this is a sed-oriented question, one approach would be to use sed itself:
sed 's/\([\[/({.*+^$?]\)/\\\1/g'
So given an arbitrary string $STRING we could write something like:
re=$(sed 's/\([\[({.*+^$?]\)/\\\1/g' <<< "$STRING")
sed "/$re/d" FILE
or as a one-liner:
sed "/$(sed 's/\([\[/({.*+^$?]\)/\\\1/g' <<< "$STRING")/d"
with variations as described elsewhere on this page.
cat filename | grep -v "pattern" > filename.1
mv filename.1 filename
You can use good old ed to edit a file in a similar fashion to the answer that uses ex. The big difference in this case is that ed takes its commands via standard input, not as command line arguments like ex can. When using it in a script, the usual way to accomodate this is to use printf to pipe commands to it:
printf "%s\n" "g/pattern/d" w | ed -s filename
or with a heredoc:
ed -s filename <<EOF
g/pattern/d
w
EOF
This solution is for doing the same operation on multiple file.
for file in *.txt; do grep -v "Matching Text" $file > temp_file.txt; mv temp_file.txt $file; done
I found most of the answers not useful for me, If you use vim I found this very easy and straightforward:
:g/<pattern>/d
Source
I can remove the first line of csv file's starting with myfile and merge them using:
sed 1d myfile*.csv > myfile_merged.csv
I'd like to also remove the last line of the csv files.
I've tried:
sed 1d -i '$d' myfile*.csv > myfile_merged.csv
But get the error:
sed: can't read $d: No such file or directory
Problem is this command:
sed 1d -i '$d' myfile*.csv > myfile_merged.csv
You need not have an argument after -i (inline replacement) in sed otherwise it is treated as a SUFFIX to create a backup for inline replacement.
What you need is this gnu sed command:
sed -i '1d;$d' myfile*.csv
This will remove 1st and last line in each of the matched file and save it in place.
What you're probably trying to do is:
sed -e '1d' -e '$d' myfile*.csv > merged.csv
But this won't work, because it tells sed to remove the first and last line of ALL files, rather than EACH file. In other words, you'll strip the first line of the first file, and the last line of the last file ... and that's it.
To process each file individually, you probably need to process each file .. individually. :)
for f in myfile*.csv
sed -e '1d;$d' "$f"
done > merged.csv
Note that while this will run in bash, it's also POSIX compatible (both the shell and sed parts). And it does not care whether your input is CSV or any other format, as long as it can be parsed line by line using sed.
I have a directory of 40 or so csv's. Each csv file has an extra 10 lines at the top that I don't need. I'm new to bash commands, but I have found that I can use
tail -n +10 oldfile.csv > newfile.csv
to cut 10 lines from a file one at a time. How can I do this across all csv's in the directory? I have tried doing this:
for filename in *foo*; do echo tail -n +10 \"$filename\" > \"${filename}\"; done
From what I've read, I thought this would pass in every csv containing foo in its name, run the formula, and leave the filename alone. Where am I going wrong?
You cannot use the same file as input and ouput.
With sed, your can edit the file in place with the -i flag:
for f in *.csv; do
sed -i '1,10d' "$f"
done
or as one-liner for the command line:
for f in *.csv; do sed -i '1,10d' "$f"; done
As a side note, your tail should be tail -n +11 to output 11th line to end of file.
Use a proper loop as below. Am using the native ex editor which Vim uses internally to in-place replacement, so you don't have to move the files back again using mv or any other command.
for file in *.csv
do
ex -sc '1d10|x' "$file"
done
The command moves to first line, selects 10 lines from first, deletes it and saves & closes the file.
Use a command-line friendly version in a single line as
for file in *.csv; do ex -sc '1d10|x' "$file"; done
The ex command is POSIX compatible and can work on all major platforms and distros.
In awk:
$ awk 'FNR>10{ print > "new-" FILENAME }' files*
Explained:
FNR>10 if current record number in current file is greater than 10, condition is true.
print well, output
> "new-" FILENAME redirect output to a new file named new-file, for example.
Edited to writing output to multiple files. Original which just outputed to screen was awk 'FNR>10' files*
I have a file, which has multiple lines.
For example:
a
ab#
ad.
a12fs
b
c
...
I want to use sed or awk delete the line, if the line include symbols or numbers. (For example, I want to delete: ab#, ad., a12fs.... lines)
or in another words, I just want to keep the line which include [a-z][A-Z] .
I know how to delete number line,
sed '/[0-9]/d' file.txt
but I do not know how to delete symbols lines.
Or there has any easy way to do that?
To keep blank lines:
grep '^[[:alpha:]]*$' file
sed '/[^[:alpha:]]/d' file
awk '/^[[:alpha:]]*$/' file
To remove blank lines:
grep '^[[:alpha:]]+$' file
sed -E -n '/^[[:alpha:]]+$/p' file
awk '/^[[:alpha:]]+$/' file
grep works well too and is even simpler: just do the reverse: keep the lines that interest you, which are way easier to define
grep -i '^[a-z]*$' file.txt
(match lines containing only letters and empty lines, and -i option makes grep case-insensitive)
to remove empty lines as well:
grep -i '^[a-z]+$' file.txt
caution when using Windows text files, as there's a carriage return at the end of the line, so nothing would match depending on grep versions (tested on windows here and it works)
but just in case:
grep -iP '^[a-z]*\r?$'
(note the P option to enable perl expressions or \r is not recognized)
You can use this sed:
sed '/^[A-Za-z0-9]\+$/!d' file
(OR)
sed '/[^A-Za-z0-9]/d' file
$ awk '!/[^[:alpha:]]/' file.txt
a
b
c