I have text files with lines like this:
U_town/u_LN0_pk_LN3_bnb_LN155/DD0 U_DESIGN/u_LNxx_pk_LN99_bnb_LN151_LN11_/DD5
U_master/u_LN999_pk_LN767888_bnb_LN9772/Dnn111 u_LN999_pk_LN767888_bnb_LN9772_LN9999_LN11/DD
...
I am trying to substitute any other character except for / to nothing and keep a word with pattern _LN\d+_ with Perl one-liner.
So the edited version would look like:
/_LN0__LN3__LN155/ /_LN99__LN151_LN11_/
/_LN999__LN767888_/ _LN999__LN767888__LN9772_LN9999_/
I tried below which returned empty lines
perl -pe 's/(?! _LN\d+_)[^\/].+//g' file
Below returned only '/'.
perl -pe 's/(?! _LN\d+_)\w+//g' file
Is it perhaps not possible with a one-liner and I should consider writing a code to parse character by character and see if a matching word _LN\d+_ or a character / is there?
To merely remove everything other than these patterns can simply match the patterns and join the matches back
perl -wnE'say join "", m{/ | _LN[0-9]+_ }gx' file
or perhaps, depending on details of the requirements
perl -wnE'say join "", m{/ | _LN[0-9]+(?=_) }gx' file
(See explanation in the last bullet below.)
Prints, for the first line (of the two) of the shown sample input
/_LN0__LN3_//_LN99__LN151_
...
or, in the second version
/_LN0_LN3//_LN99_LN151_LN11/
...
The _LN155 is not there because it is not followed by _. See below.
Questions:
Why are there spaces after some / in the "edited version" shown in the question?
The pattern to keep is shown as _LN\d+_ but _LN155 is shown to be kept even though it is not followed by a _ in the input (but by a /) ...?
Are underscores optional by any chance? If so, append ? to them in the pattern
perl -wnE'say join "", m{/ | _?LN[0-9]+_? }gx' file
with output
/_LN0__LN3__LN155//_LN99__LN151_LN11_/
(It's been clarified that the extra space in the shown desired output is a mistake.)
If the underscores "overlap," like in _LN155_LN11_, in the regex they won't be both matched by the _LN\d+_ pattern, since the first one "takes" the underscore.
But if such overlapping instances nned be kept then replace the trailing _ with a lookahead for it, which doesn't consume it so it's there for the leading _ on the next pattern
perl -wnE'say join "", m{/ | _LN[0-9]+(?=_) }gx' file
(if the underscores are optional and you use _?LN\d+_? pattern then this isn't needed)
I'm trying to remove double quotes that appear within a string coming from a dB because it's causing an stream error in another application. I can't clean up the dB to remove these, so I need to replace the character on the fly.
I've tried using sed, ssed, and perl all without success. This regular expression is locating the problem quotes, but when I plug it into sed to replace them with a single quote my output still contains the double quote.
sed "s/(\?<\!\t|^)\"(\?\!\t|$)/'/g" test.txt
I'm on Mac, if this looks a bit odd.
The regex is valid, but when I test on a tab-delimited file containing this:
"foo" "rea"son" "text's"
My output is identical to the above. Any idea what I'm doing wrong?
Thanks
I assume you want to turn all occurrences of " that are not on a field boundary (i.e. either preceded or succeeded by either a tab or the beginning/end of the string) by '.
This can be done using perl and the following substitution:
s/(?<=[^\t])"(?=[^\t\n])/'/g;
(With sed this is not directly possible as it does not support look-behind / look-ahead assertions.)
To use this code on the command line, it needs to be escaped for whatever shell you're using. Assuming bash or a similar sh-like shell:
perl -pe 's/(?<=[^\t])"(?=[^\t\n])/'\''/g' test.txt
Here I use '...' to quote most of the code. To get a single ' into the quoted string, I leave the quoted area ...', add an escaped single quote \', and switch back into a single-quoted string '.... That's why a literal ' turns into '\'' on the command line.
I am new to coding and I'm trying to format some bioinformatics data. I am trying to remove all the spaces after GT:GL:GOF:GQ:NR:NV with commas, but not anything outside of the format xx:xx:xx:xx:xx (like the example). I know I need to use sed with regex option but I'm not very familiar with how to use it. I've never actually used sed before and got confused trying so any help would be appreciated. Sorry if I formatted this poorly (this is my first post).
EDIT 2: I got actual data from the file this time which may help solve the problem. Removed the bad example.
New Example: I pulled this data from my actual file (this is just two samples), and it is surrounded by other data. Essentially the line has a bunch of data followed by "GT:GL:GOF:GQ:NR:NV ", after this there is more data in the format shown below, and finally there is some more random data. Unfortunately I can't post a full line of the data because it is extremely long and will not fit.
Input
0/1:-1,-1,-1:146:28:14,14:4,0 0/1:-1,-1,-1:134:6:2,2:1,0
Output
0/1:-1,-1,-1:146:28:14,14:4,0,0/1:-1,-1,-1:134:6:2,2:1,0
With Basic Regular Expressions, you can use character classes and backreferences to accomplish your task, e.g.
$ sed 's/\([0-9][0-9]*:[0-9][0-9]*\)[ ]\([0-9][0-9]*:[0-9][0-9]*\)/\1,\2/g' file
1/0 ./. 0/1 GT:GL:GOF:GQ:NR:NV 1:12:314,213:132:13:31,14:31:31 AB GT BB
1/0 ./. 0/1 GT:GL:GOF:GQ:NR:NV 10:13:12,41:41:1:13,13:131:1:1 AB GT RT
1/0 ./. 0/1 GT:GL:GOF:GQ:NR:NV 1:12:314,213:132:13:31,14:31:31 AB GT
Which basically says:
find and capture any [0-9][0-9]* one or more digits,
separated by a :, and
followed by [0-9][0-9]* one or more digits -- as capture group 1,
match a space following capture group 1 followed by capture group 2 (which is the same as capture group 1),
then replace the space separating the capture groups with a comma reinserting the capture group text using backreference 1 and 2 (e.g. \1 and \2), finally
make the replacement global (e.g. g) to replace all matching occurrences.
Edit Based On New Input Posted
If you still need all of the original commas added, and you now want to add a comma between ,0 0/ (where there is a comma precedes a single-digit followed by the space to be replaced with a comma, followed by a single-digit and a forward-slash), then all you need to do is make your capture groups conditional (on either capturing the original data as above -or- capturing this new segment. You do that by including an OR (e.g. \| in basic regex terms) between the conditions.
For instance by adding \|,[0-9] at the end of the first capture group and \|[0-9][/] at the end of the second, e.g.
$ sed 's/\([0-9][0-9]*:[0-9][0-9]*\|,[0-9]\)[ ]\([0-9][0-9]*:[0-9][0-9]*\|[0-9][/]\)/\1,\2/g' file
0/1:-1,-1,-1:146:28:14,14:4,0,0/1:-1,-1,-1:134:6:2,2:1,0
If you have other caveats in your file, I suggest you post several complete lines of input, and if they are too long, then create a zip, gzip, bzip or xz file and post it to a site like pastebin and add the link to your question.
If all you really care about now is the space in ,0 0/, then you can shorten the sed command to:
$ sed 's/\(,[0-9]\)[[:space:]]\([0-9][/]\)/\1,\2/g' file
0/1:-1,-1,-1:146:28:14,14:4,0,0/1:-1,-1,-1:134:6:2,2:1,0
(note: I've included [[:space:]] to handle any whitespace (space, tab, ...) instead of just the literal [ ] (space) in the new example)
Let me know if this fixes the issue.
I'm assuming that the xx:xx:xx or xx:xx:xx:xx can have any number of parts, since some have 3, and some have 4.
This is quite difficult to do reliably with sed, as it does not support lookarounds, which seem like they might be needed for this example.
You can try something like:
perl -pe 's/(?<=\d) (?=\d+(:\d+){2,})/,/g' input.txt
If you've got your heart set on sed, you can try this, but it may miss some cases:
sed -r 's/(:[0-9]+) ([0-9]+:)/\1,\2/g' input.txt
Could you please try following. This will take care of printing those values also which are NOT coming in match of regex. Also we would have made regex mentioned in match a bit shorter by doing it as [0-9]+\.{4} etc since this is tested on old awk so couldn't test it.
awk '
BEGIN{
OFS=","
}
match($0,/GT:GL:GOF:GQ:NR:NV [0-9]+:[0-9]+:[0-9]+:[0-9]+:[0-9]+/){
value=substr($0,RSTART!=1?1:RSTART,RSTART+RLENGTH-1)
value1=substr($0,RSTART+RLENGTH+1)
gsub(/[[:space:]]+/,",",value1)
print value,value1
next
}
1
' Input_file
You may also achieve your desired result without regex, using awk:
awk '{printf "%s", $1FS$2FS$3FS$4FS$5","$6","$7; for (i=8;i<=NF;i++) printf "%s", FS$i; print ""}' input.txt
Basically, it outputs from field 1 to 5 with the default field separator ("space"), then from field 5 to 7 with the comma separator, then from field 8 onwards with default separator again.
perl myscript.pl '0/1:-1,-1,-1:146:28:14,14:4,0 0/1:-1,-1,-1:134:6:2,2:1,0'
myscript.pl,
#!/usr/local/ActivePerl-5.20/bin/env perl
my $input = $ARGV[0];
$input =~ s/ /\,/g;
print $input, "\n";
__DATA__
output
0/1:-1,-1,-1:146:28:14,14:4,0,0/1:-1,-1,-1:134:6:2,2:1,0
This will remove all spaces, not just the space in question
I would like to replace all { } on a certain line with [ ], but unfortunately I am only able to match the last occurrence of the regexp.
I have a config file which has structure as follows:
entry {
id 123456789
desc This is a description of {foo} and was added by {bar}
trigger 987654321
}
I have the following sed, of which is able to replace the last match 'bar' but not 'foo':
sed s'/\(desc.*\){\(.*\)}/\1\[\2\]/g' < filename
I anchor this search to the line containing 'desc' as I would hate for it to replace the delimiting braces of each 'entry' block.
For the life of me I am unable to figure out how to replace all of the occurrences.
Any help is appreciated - have been learning all day and unable to read any more tutorials for fear that my corneas might crack.
Thanks!
Try the following:
sed '/desc/ s/{\([^}]*\)}/[\1]/g' filename
The search and replace in the above command will only be done for lines that match the regex /desc/, however I don't think this is actually necessary because sed processes text a line at a time, so even without this you wouldn't be replacing braces on the 'entry' block. This means that you could probably simplify this to the following:
sed 's/{\([^}]*\)}/[\1]/g' filename
Instead of .* inside of the capturing group [^}]* is used which will match everything except closing braces, that way you won't match from the first opening to the last closing.
Also, you can just provide the file name as the final argument to sed instead of using input redirection.
I'm getting totally lost in shell programming, mainly because every site I use offers different tool to do pattern matching. So my question is what tool to use to do simple pattern matching in piped stream.
context: I have named.conf file, and i need all zones names in a simple file for further processing. So I do ~$ cat named.local | grep zone and get totally lost here. My output is ~hundred or so newlines in form 'zone "domain.tld" {' and I need text in double quotes.
Thanks for showing a way to do this.
J
I think what you're looking for is sed... it's a stream editor which will let you do replacements on a line-by-line basis.
As you're explaining it, the command `cat named.local | grep zone' gives you an output a little like this:
zone "domain1.tld" {
zone "domain2.tld" {
zone "domain3.tld" {
zone "domain4.tld" {
I'm guessing you want the output to be something like this, since you said you need the text in double quotes:
"domain1.tld"
"domain2.tld"
"domain3.tld"
"domain4.tld"
So, in reality, from each line we just want the text between the double-quotes (including the double-quotes themselves.)
I'm not sure you're familiar with Regular Expressions, but they are an invaluable tool for any person writing shell scripts. For example, the regular expression /.o.e/ would match any line where there's a word with the 2nd letter was a lower-case o, and the 4th was e. This would match string containing words like "zone", "tone", or even "I am tone-deaf."
The trick there was to use the . (dot) character to mean "any letter". There's a couple of other special characters, such as * which means "repeat the previous character 0 or more times". Thus a regular expression like a* would match "a", "aaaaaaa", or an empty string: ""
So you can match the string inside the quotes using: /".*"/
There's another thing you would know about sed (and by the comments, you already do!) - it allows backtracking. Once you've told it how to recognize a word, you can have it use that word as part of the replacement. For example, let's say that you wanted to turn this list:
Billy "The Kid" Smith
Jimmy "The Fish" Stuart
Chuck "The Man" Norris
Into this list:
The Kid
The Fish
The Man
First, you'd look for the string inside the quotes. We already saw that, it was /".*"/.
Next, we want to use what's inside the quotes. We can group it using parens: /"(.*)"/
If we wanted to replace the text with the quotes with an underscore, we'd do a replace: s/"(.*)"/_/, and that would leave us with:
Billy _ Smith
Jimmy _ Stuart
Chuck _ Norris
But we have backtracking! That'll let us recall what was inside the parens, using the symbol \1. So if we do now: s/"(.*)"/\1/ we'll get:
Billy The Kid Smith
Jimmy The Fish Stuart
Chuck The Man Norris
Because the quotes weren't in the parens, they weren't part of the contents of \1!
To only leave the stuff inside the double-quotes, we need to match the entire line. To do that we have ^ (which means "beginning of line"), and $ (which means "end of line".)
So now if we use s/^.*"(.*)".*$/\1/, we'll get:
The Kid
The Fish
The Man
Why? Let's read the regular expression s/^.*"(.*)".*$/\1/ from left-to-right:
s/ - Start a substitution regular expression
^ - Look for the beginning of the line. Start from there.
.* - Keep going, reading every character, until...
" - ... until you reach a double-quote.
( - start a group a characters we might want to recall later when backtracking.
.* - Keep going, reading every character, until...
) - (pssst! close the group!)
" - ... until you reach a double-quote.
.* - Keep going, reading every character, until...
$ - The end of the line!
/ - use what's after this to replace what you matched
\1 - paste the contents of the first group (what was in the parens) matched.
/ - end of regular expression
In plain English: "Read the entire line, copying aside the text between the double-quotes. Then replace the entire line with the content between the double qoutes."
You can even add double-quote around the replacing text s/^.*"(.*)".*$/"\1"/, so we'll get:
"The Kid"
"The Fish"
"The Man"
And that can be used by sed to replace the line with the content from within the quotes:
sed -e "s/^.*\"\(.*\)\".*$/\"\1\"/"
(This is just shell-escaped to deal with the double-quotes and slashes and stuff.)
So the whole command would be something like:
cat named.local | grep zone | sed -e "s/^.*\"\(.*\)\".*$/\"\1\"/"
Well, nobody mentioned cut yet, so, to prove that there are many ways to do something with the shell:
% grep '^zone' /etc/bind/named.conf | cut -d' ' -f2
"gennic.net"
"generic-nic.net"
"dyn.generic-nic.net"
"langtag.net"
1.
zoul#naima:etc$ cat named.conf | grep zone
zone "." IN {
zone "localhost" IN {
file "localhost.zone";
zone "0.0.127.in-addr.arpa" IN {
2.
zoul#naima:etc$ cat named.conf | grep ^zone
zone "." IN {
zone "localhost" IN {
zone "0.0.127.in-addr.arpa" IN {
3.
zoul#naima:etc$ cat named.conf | grep ^zone | sed 's/.*"\([^"]*\)".*/\1/'
.
localhost
0.0.127.in-addr.arpa
The regexp is .*"\([^"]*\)".*, which matches:
any number of any characters: .*
a quote: "
starts to remember for later: \(
any characters except quote: [^"]*
ends group to remember: \)
closing quote: "
and any number of characters: .*
When calling sed, the syntax is 's/what_to_match/what_to_replace_it_with/'. The single quotes are there to keep your regexp from being expanded by bash. When you “remember” something in the regexp using parens, you can recall it as \1, \2 etc. Fiddle with it for a while.
You should have a look at awk.
As long as someone is pointing out sed/awk, I'm going to point out that grep is redundant.
sed -ne '/^zone/{s/.*"\([^"]*\)".*/\1/;p}' /etc/bind/named.conf
This gives you what you're looking for without the quotes (move the quotes inside the parenthesis to keep them). In awk, it's even simpler with the quotes:
awk '/^zone/{print $2}' /etc/bind/named.conf
I try to avoid pipelines as much as possible (but not more). Remember, Don't pipe cat. It's not needed. And, insomuch as awk and sed duplicating grep's work, don't pipe grep, either. At least, not into sed or awk.
Personally, I'd probably have used perl. But that's because I probably would have done the rest of whatever you're doing in perl, making it a minor detail (and being able to slurp the whole file in and regex against everything simultaneously, ignoring \n's would be a bonus for cases where I don't control /etc/bind, such as on a shared webhost). But, if I were to do it in shell, one of the above two would be the way I'd approach it.