grep (awk) a file from A to first empty line - bash

I need to grep a file from a line containing Pattern A to a first empty line.
I used awk but I don't know how to code this empty line.
cat ${file} | awk '/Pattern A/,/Pattern B/'

sed might be best:
sed -n '/PATTERN/,/^$/p' file
To avoid printing the empty line:
sed -n '/PATTERN/,/^$/{/^$/d; p}' file
or even better - thanks jthill!:
sed -n '/PATTERN/,/^$/{/./p}' file
Above solutions will give more output than needed if PATTERN appears more than once. For that, it is best to quit after empty line is found, as jaypal's answer suggests:
sed -n '/PATTERN/,/^$/{/^$/q; p}' file
Explanation
^$ matches empty lines, because ^ stands for beginning of line and $ for end of line. So that, ^$ means: lines not containing anything in between beginning and end of line.
/PATTERN/,/^$/{/^$/d; p}
/PATTERN/,/^$/ match lines from PATTERN to empty line.
{/^$/d; p} remove (d) the lines being on ^$ format, print (p) the rest.
{/./p} just prints those lines having at least one character.
With awk you can use:
awk '!NF{f=0} /PATTERN/ {f=1} f' file
Same as sed, if it has many lines with PATTERN it would fail. For this, let's exit once empty line is found:
awk 'f && !NF{exit} /PATTERN/ {f=1} f' file
Explanation
!NF{f=0} if there are no fields (that is, line is empty), unset the flag f.
/PATTERN/ {f=1} if PATTERN is found, set the flag f.
f if flag f is set, this is True, so it performs the default awk behaviour: print the line.
Test
$ cat a
aa
bb
hello
aaaaaa
bbb
ttt
$ awk '!NF{f=0} /hello/ {f=1} f' a
hello
aaaaaa
bbb
$ sed -n '/hello/,/^$/{/./p}' a
hello
aaaaaa
bbb

Using sed:
sed -n '/PATTERN/,/^$/{/^$/q;p;}' file
Using regex range, you define your range from the PATTERN to blank line (/^$/). When you encounter a blank line, you quit else you keep printing.
Using awk:
awk '/PATTERN/{p=1}/^$/&&p{exit}p' file
You enable a flag when you encounter your PATTERN. When you reach a blank line and flag is enabled, you exit. If not, you keep printing.
Another alternate suggested by devnull in the comments is to use pcregrep:
pcregrep -M 'PATTERN(.|\n)*?(?=\n\n)' file

I think this is a nice, readable Perl one-liner:
perl -wne '$f=1 if /Pattern A/; exit if /^\s*$/; print if $f' file
Set the flag $f when the pattern is matched
Exit if a blank line (only whitespace between start and end of line) is found
Print the line if the flag is set
Testing it out:
$ cat file
1
2
Pattern A
3
4
5
6
7
8
9
$ perl -wne '$f=1 if /Pattern A/; exit if /^$/; print if $f' file
Pattern A
3
4
5
6
Alternatively, based on the suggestion by #jaypal, you could do this:
perl -lne '/Pattern A/ .. 1 and !/^$/ ? print : exit' file
Rather than using a flag $f, the range operator .. takes care of this for you. It evaluates to true when "Pattern A" is found on the line and remains true indefinitely. When it is true, the other part will be evaluated and will print until a blank line is found.

Never use
/foo/,/bar/
in awk unless you want to get from the first occurrence of "foo" to the last occurrence of "bar" as it makes trivial jobs marginally briefer but even slightly more interesting requirements require a complete re-write.
Just use:
/foo/{f=1} f{print; if (/bar/) f=0}
or similar instead.
In the case the awk solution is:
awk '/pattern/{f=1} f{print; if (!NF) exit}' file

Related

bash / sed : editing of the file

I use sed to remove all lines starting from "HETATM" from the input file and cat to combine another file with the output recieved from SED
sed -i '/^HETATM/ d' file1.pdb
cat fil2.pdb file1.pdb > file3.pdb
is this way to do it in one line e.g. using only sed?
If you want to consider awk then it can be done in a single command:
awk 'FNR == NR {print; next} !/^HETATM/' file2.pdb file1.pdb > file3.pdb
With cat + grep combination please try following code. Simple explanation would be, using cat command's capability to concatenate file's output when multiple files are passed to it and using grep -v to remove all words starting from HETATM in file1.pdb before sending is as an input to cat command and creating new file named file3.pdb from cat command's output.
cat file2.pdb <(grep -v '^HETATM' file1.pdb) > file3.pdb
I'm not sure what you mean by "remove all lines starting from 'HETATM'", but if you mean that any line that appears in the file after a line that starts with "HETATM" will not be outputted, then your sed expression won't do it - it will just remove all lines starting with the pattern while leaving all following lines that do not start with the pattern.
There are ways to get the effect I believe you wanted, possibly even with sed - but I don't know sed all that well. In perl I'd use the range operator with a guaranteed non-matching end expression (not sure what will be guaranteed for your input, I used "XXX" in this example):
perl -ne 'unless (/^HETATM/../XXX/) { print; }' file1.pdb
mawk '(FNR == NR) < NF' FS='^HETATM' f1 f2

How to add 100 spaces at end of each line of a file in Unix

I have a file which is supposed to contain 200 characters in each line. I received a source file with only 100 characters in each line. I need to add 100 extra white spaces to each line now. If it were few blank spaces, we could have used sed like:
sed 's/$/ /' filename > newfilename
Since it's 100 spaces, can anyone tell me is it possible to add in Unix?
If you want to have fixed n chars per line (don't trust the input file has exact m chars per line) follow this. For the input file with varying number of chars per line:
$ cat file
1
12
123
1234
12345
extend to 10 chars per line.
$ awk '{printf "%-10s\n", $0}' file | cat -e
1 $
12 $
123 $
1234 $
12345 $
Obviously change 10 to 200 in your script. Here $ shows end of line, it's not there as a character. You don't need cat -e, here just to show the line is extended.
With awk
awk '{printf "%s%100s\n", $0, ""}' file.dat
$0 refers to the entire line.
Updated after Glenn's suggestion
Somewhat how Glenn suggests in the comments, the substitution is unnecessary, you can just add the spaces - although, taking that logic further, you don't even need the addition, you can just say them after the original line.
perl -nlE 'say $_," "x100' file
Original Answer
With Perl:
perl -pe 's/$/" " x 100/e' file
That says... "Substitute (s) the end of each line ($) with the calculated expression (e) of 100 repetitions of a space".
If you wanted to pad all lines to, say, 200 characters even if the input file was ragged (all lines of differing length), you could use something like this:
perl -pe '$pad=200-length;s/$/" " x $pad/e'
which would make up lines of 83, 102 and 197 characters to 200 each.
If you use Bash, you can still use sed, but use some readline functionality to keep you from manually typing 100 spaces (see manual for "Readline arguments").
You start typing normally:
sed 's/$/
Now, you want to insert 100 spaces. You can do this by prepending hitting the space bar with a readline argument to indicate that you want it to happen 100 times, i.e., you manually enter what would look like this as a readline keybinding:
M-1 0 0 \040
Or, if your meta key is the alt key: Alt+1 00Space
This inserts 100 spaces, and you get
sed 's/$/ /' filename
after typing the rest of the command.
This is useful for working in an interactive shell, but not very pretty for scripts – use any of the other solutions for that.
Just in case you are looking for a bash solution,
while IFS= read -r line
do
printf "%s%100s\n" "$line"
done < file > newfile
Test
Say I have a file with 3 lines it it as
$ wc -c file
16 file
$ wc -c newfile
316 newfile
Original Answer
spaces=$(echo {1..101} | tr -d 0-9)
while read line
do
echo -e "${line}${spaces}\n" >> newfile
done < file
You can use printf in awk:
awk '{printf "%s%*.s\n", $0, 100, " "}' filename > newfile
This printf will append 100 spaces at the end of each newline.
Another way in GNU awk using string-manipulation function sprintf.
awk 'BEGIN{s=sprintf("%-100s", "");}{print $0 s}' input-file > file-with-spaces
A proof with an example:-
$ cat input-file
1234jjj hdhyvb 1234jjj
6789mmm mddyss skjhude
khora77 koemm sado666
nn1004 nn1004 457fffy
$ wc -c input-file
92 input-file
$ awk 'BEGIN{s=sprintf("%-100s", "");}{print $0 s}' input-file > file-with-spaces
$ wc -c file-with-spaces
492 file-with-spaces

Bash - remove all lines beginning with 'P'

I have a text file that's about 300KB in size. I want to remove all lines from this file that begin with the letter "P". This is what I've been using:
> cat file.txt | egrep -v P*
That isn't outputting to console. I can use cat on the file without another other commands and it prints out fine. My final intention being to:
> cat file.txt | egrep -v P* > new.txt
No error appears, it just doesn't print anything out and if I run the 2nd command, new.txt is empty.
I should say I'm running Windows 7 with Cygwin installed.
Explanation
use ^ to anchor your pattern to the beginning of the line ;
delete lines matching the pattern using sed and the d flag.
Solution #1
cat file.txt | sed '/^P/d'
Better solution
Use sed-only:
sed '/^P/d' file.txt > new.txt
With awk:
awk '!/^P/' file.txt
Explanation
The condition starts with an ! (negation), that negates the following pattern ;
/^P/ means "match all lines starting with a capital P",
So, the pattern is negated to "ignore lines starting with a capital P".
Finally, it leverage awk's behavior when { … } (action block) is missing, that is to print the record validating the condition.
So, to rephrase, it ignores lines starting with a capital P and print everything else.
Note
sed is line oriented and awk column oriented. For your case you should use the first one, see Edouard Lopez's reponse.
Use sed with inplace substitution (for GNU sed, will also for your cygwin)
sed -i '/^P/d' file.txt
BSD (Mac) sed
sed -i '' '/^P/d' file.txt
Use start of line mark and quotes:
cat file.txt | egrep -v '^P.*'
P* means P zero or more times so together with -v gives you no lines
^P.* means start of line, then P, and any char zero or more times
Quoting is needed to prevent shell expansion.
This can be shortened to
egrep -v ^P file.txt
because .* is not needed, therefore quoting is not needed and egrep can read data from file.
As we don't use extended regular expressions grep will also work fine
grep -v ^P file.txt
Finally
grep -v ^P file.txt > new.txt
This works:
cat file.txt | egrep -v -e '^P'
-e indicates expression.

How to get the part of a file after the first line that matches a regular expression

I have a file with about 1000 lines. I want the part of my file after the line which matches my grep statement.
That is:
cat file | grep 'TERMINATE' # It is found on line 534
So, I want the file from line 535 to line 1000 for further processing.
How can I do that?
The following will print the line matching TERMINATE till the end of the file:
sed -n -e '/TERMINATE/,$p'
Explained: -n disables default behavior of sed of printing each line after executing its script on it, -e indicated a script to sed, /TERMINATE/,$ is an address (line) range selection meaning the first line matching the TERMINATE regular expression (like grep) to the end of the file ($), and p is the print command which prints the current line.
This will print from the line that follows the line matching TERMINATE till the end of the file:
(from AFTER the matching line to EOF, NOT including the matching line)
sed -e '1,/TERMINATE/d'
Explained: 1,/TERMINATE/ is an address (line) range selection meaning the first line for the input to the 1st line matching the TERMINATE regular expression, and d is the delete command which delete the current line and skip to the next line. As sed default behavior is to print the lines, it will print the lines after TERMINATE to the end of input.
If you want the lines before TERMINATE:
sed -e '/TERMINATE/,$d'
And if you want both lines before and after TERMINATE in two different files in a single pass:
sed -e '1,/TERMINATE/w before
/TERMINATE/,$w after' file
The before and after files will contain the line with terminate, so to process each you need to use:
head -n -1 before
tail -n +2 after
IF you do not want to hard code the filenames in the sed script, you can:
before=before.txt
after=after.txt
sed -e "1,/TERMINATE/w $before
/TERMINATE/,\$w $after" file
But then you have to escape the $ meaning the last line so the shell will not try to expand the $w variable (note that we now use double quotes around the script instead of single quotes).
I forgot to tell that the new line is important after the filenames in the script so that sed knows that the filenames end.
How would you replace the hardcoded TERMINATE by a variable?
You would make a variable for the matching text and then do it the same way as the previous example:
matchtext=TERMINATE
before=before.txt
after=after.txt
sed -e "1,/$matchtext/w $before
/$matchtext/,\$w $after" file
to use a variable for the matching text with the previous examples:
## Print the line containing the matching text, till the end of the file:
## (from the matching line to EOF, including the matching line)
matchtext=TERMINATE
sed -n -e "/$matchtext/,\$p"
## Print from the line that follows the line containing the
## matching text, till the end of the file:
## (from AFTER the matching line to EOF, NOT including the matching line)
matchtext=TERMINATE
sed -e "1,/$matchtext/d"
## Print all the lines before the line containing the matching text:
## (from line-1 to BEFORE the matching line, NOT including the matching line)
matchtext=TERMINATE
sed -e "/$matchtext/,\$d"
The important points about replacing text with variables in these cases are:
Variables ($variablename) enclosed in single quotes ['] won't "expand" but variables inside double quotes ["] will. So, you have to change all the single quotes to double quotes if they contain text you want to replace with a variable.
The sed ranges also contain a $ and are immediately followed by a letter like: $p, $d, $w. They will also look like variables to be expanded, so you have to escape those $ characters with a backslash [\] like: \$p, \$d, \$w.
As a simple approximation you could use
grep -A100000 TERMINATE file
which greps for TERMINATE and outputs up to 100,000 lines following that line.
From the man page:
-A NUM, --after-context=NUM
Print NUM lines of trailing context after matching lines.
Places a line containing a group separator (--) between
contiguous groups of matches. With the -o or --only-matching
option, this has no effect and a warning is given.
A tool to use here is AWK:
cat file | awk 'BEGIN{ found=0} /TERMINATE/{found=1} {if (found) print }'
How does this work:
We set the variable 'found' to zero, evaluating false
if a match for 'TERMINATE' is found with the regular expression, we set it to one.
If our 'found' variable evaluates to True, print :)
The other solutions might consume a lot of memory if you use them on very large files.
If I understand your question correctly you do want the lines after TERMINATE, not including the TERMINATE-line. AWK can do this in a simple way:
awk '{if(found) print} /TERMINATE/{found=1}' your_file
Explanation:
Although not best practice, you could rely on the fact that all variables defaults to 0 or the empty string if not defined. So the first expression (if(found) print) will not print anything to start off with.
After the printing is done, we check if this is the starter-line (that should not be included).
This will print all lines after the TERMINATE-line.
Generalization:
You have a file with start- and end-lines and you want the lines between those lines excluding the start- and end-lines.
start- and end-lines could be defined by a regular expression matching the line.
Example:
$ cat ex_file.txt
not this line
second line
START
A good line to include
And this line
Yep
END
Nope more
...
never ever
$ awk '/END/{found=0} {if(found) print} /START/{found=1}' ex_file.txt
A good line to include
And this line
Yep
$
Explanation:
If the end-line is found no printing should be done. Note that this check is done before the actual printing to exclude the end-line from the result.
Print the current line if found is set.
If the start-line is found then set found=1 so that the following lines are printed. Note that this check is done after the actual printing to exclude the start-line from the result.
Notes:
The code rely on the fact that all AWK variables defaults to 0 or the empty string if not defined. This is valid, but it may not be best practice so you could add a BEGIN{found=0} to the start of the AWK expression.
If multiple start-end-blocks are found, they are all printed.
grep -A 10000000 'TERMINATE' file
is much, much faster than sed, especially working on really a big file. It works up to 10M lines (or whatever you put in), so there isn't any harm in making this big enough to handle about anything you hit.
Use Bash parameter expansion like the following:
content=$(cat file)
echo "${content#*TERMINATE}"
There are many ways to do it with sed or awk:
sed -n '/TERMINATE/,$p' file
This looks for TERMINATE in your file and prints from that line up to the end of the file.
awk '/TERMINATE/,0' file
This is exactly the same behaviour as sed.
In case you know the number of the line from which you want to start printing, you can specify it together with NR (number of record, which eventually indicates the number of the line):
awk 'NR>=535' file
Example
$ seq 10 > a #generate a file with one number per line, from 1 to 10
$ sed -n '/7/,$p' a
7
8
9
10
$ awk '/7/,0' a
7
8
9
10
$ awk 'NR>=7' a
7
8
9
10
If for any reason, you want to avoid using sed, the following will print the line matching TERMINATE till the end of the file:
tail -n "+$(grep -n 'TERMINATE' file | head -n 1 | cut -d ":" -f 1)" file
And the following will print from the following line matching TERMINATE till the end of the file:
tail -n "+$(($(grep -n 'TERMINATE' file | head -n 1 | cut -d ":" -f 1)+1))" file
It takes two processes to do what sed can do in one process, and if the file changes between the execution of grep and tail, the result can be incoherent, so I recommend using sed. Moreover, if the file doesn’t not contain TERMINATE, the first command fails.
Alternatives to the excellent sed answer by jfg956, and which don't include the matching line:
awk '/TERMINATE/ {y=1;next} y' (Hai Vu's answer to 'grep +A': print everything after a match)
awk '/TERMINATE/ ? c++ : c' (Steven Penny's answer to 'grep +A': print everything after a match)
perl -ne 'print unless 1 .. /TERMINATE/' (tchrist's answer to 'grep +A': print everything after a match)
This could be one way of doing it. If you know in what line of the file you have your grep word and how many lines you have in your file:
grep -A466 'TERMINATE' file
sed is a much better tool for the job:
sed -n '/re/,$p' file
where re is a regular expression.
Another option is grep's --after-context flag. You need to pass in a number to end at, using wc on the file should give the right value to stop at. Combine this with -n and your match expression.
This will print all lines from the last found line "TERMINATE" till the end of the file:
LINE_NUMBER=`grep -o -n TERMINATE $OSCAM_LOG | tail -n 1 | sed "s/:/ \\'/g" | awk -F" " '{print $1}'`
tail -n +$LINE_NUMBER $YOUR_FILE_NAME

How to ignore all lines before a match occurs in bash?

I would like ignore all lines which occur before a match in bash (also ignoring the matched line. Example of input could be
R1-01.sql
R1-02.sql
R1-03.sql
R1-04.sql
R2-01.sql
R2-02.sql
R2-03.sql
and if I match R2-01.sql in this already sorted input I would like to get
R2-02.sql
R2-03.sql
Many ways possible. For example: assuming that your input is in list.txt
PATTERN="R2-01.sql"
sed "0,/$PATTERN/d" <list.txt
because, the 0,/pattern/ works only on GNU sed, (e.g. doesn't works on OS X), here is an tampered solution. ;)
PATTERN="R2-01.sql"
(echo "dummy-line-to-the-start" ; cat - ) < list.txt | sed "1,/$PATTERN/d"
This will add one dummy line to the start, so the real pattern must be on line the 1 or higher, so the 1,/pattern/ will works - deleting everything from the line 1 (dummy one) up to the pattern.
Or you can print lines after the pattern and delete the 1st, like:
sed -n '/pattern/,$p' < list.txt | sed '1d'
with awk, e.g.:
awk '/pattern/,0{if (!/pattern/)print}' < list.txt
or, my favorite use the next perl command:
perl -ne 'print unless 1../pattern/' < list.txt
deletes the 1.st line when the pattern is on 1st line...
another solution is reverse-delete-reverse
tail -r < list.txt | sed '/pattern/,$d' | tail -r
if you have the tac command use it instead of tail -r The interesant thing is than the /pattern/,$d' works on the last line but the1,/pattern/d` doesn't on the first.
How to ignore all lines before a match occurs in bash?
The question headline and your example don't quite match up.
Print all lines from "R2-01.sql" in sed:
sed -n '/R2-01.sql/,$p' input_file.txt
Where:
-n suppresses printing the pattern space to stdout
/ starts and ends the pattern to match (regular expression)
, separates the start of the range from the end
$ addresses the last line in the input
p echoes the pattern space in that range to stdout
input_file.txt is the input file
Print all lines after "R2-01.sql" in sed:
sed '1,/R2-01.sql/d' input_file.txt
1 addresses the first line of the input
, separates the start of the range from the end
/ starts and ends the pattern to match (regular expression)
$ addresses the last line in the input
d deletes the pattern space in that range
input_file.txt is the input file
Everything not deleted is echoed to stdout.
This is a little hacky, but it's easy to remember for quickly getting the output you need:
$ grep -A99999 $match $file
Obviously you need to pick a value for -A that's large enough to match all contents; if you use a too-small value the output will be silently truncated.
To ensure you get all output you can do:
$ grep -A$(wc -l $file) $match $file
Of course at that point you might be better off with the sed solutions, since they don't require two reads of the file.
And if you don't want the matching line itself, you can simply pipe this command into tail -n+1 to skip the first line of output.
awk -v pattern=R2-01.sql '
print_it {print}
$0 ~ pattern {print_it = 1}
'
you can do with this,but i think jomo666's answer was better.
sed -nr '/R2-01.sql/,${/R2-01/d;p}' <<END
R1-01.sql
R1-02.sql
R1-03.sql
R1-04.sql
R2-01.sql
R2-02.sql
R2-03.sql
END
Perl is another option:
perl -ne 'if ($f){print} elsif (/R2-01\.sql/){$f++}' sql
To pass in the regex as an argument, use -s to enable a simple argument parser
perl -sne 'if ($f){print} elsif (/$r/){$f++}' -- -r=R2-01\\.sql file
This can be accomplished with grep, by printing a large enough context following the $match. This example will output the first matching line followed by 999,999 lines of "context".
grep -A999999 $match $file
For added safety (in case the $match begins with a hyphen, say) you should use -e to force $match to be used as an expression.
grep -A999999 -e '$match' $file

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