Backreference with sed - regex

I am trying to rearrange headers in my fasta file. I thought I could select the first 10 characters, then the rest of the line, and then backreference the first selection to move it to the end.
AY843768_1 Genus species 12S
would then be
Genus species 12S AY843768_1
I need to use sed for a learning exercise, but I am unsure how to make the selections to switch the 10-digit ID to the end of the line for every header in my file.
sed ‘s/^\(.\{10\}\)(.*$)/\2 \1/g' file1.fasta > file2.fasta

This will do it:
sed 's/^\(.\{10\}\) \(.*\)/\2 \1/' file1.fasta > file2.fasta
backslashes at the second braces where missing.
.* already matches the rest of the line so $ isn't needed
g isnt needed cause multiple matches per line arent possible if expression begins with ^
Anyway, using ERE instead of BRE makes it more readable:
sed -E 's/^(.{10}) (.*)/\2 \1/' file1.fasta > file2.fasta
OT: Same (or similar) can be achieved with bash only:
while read id rest;do echo "$rest $id";done <file1.fasta >file2.fasta

Related

Using grep to extract very specific strings from binary file

I have a large binary file. I want to extract certain strings from it and copy them to a new text file.
For example, in:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^G
I want to take the number '7' (after the #^#^#E) and every character after it stopping at the Z ('ignoring the M-^G).
I want to copy this 7cacscKLrrok9bwC3Z64NTnZ to a new file.
There will be multiple such strings in one file. The end will always be denoted by the M- (which I don't want copied). The start will always be denoted by a 7 (which I do want copied).
Unfortunately, my knowledge of grep, sed, etc, does not extend to this level. Can someone please suggest a viable way to achieve this?
cat -v filename | grep [7][A-Z,a-z] will show all strings with a '7' followed by a letter but that's not much.
Thank you.
I've noticed that my requirements are rather more complicated.
(I've performed the correct - I hope - formatting this time). Thanks to 'tshiono' for his (?) answer to the earlier submission.
I want to check the ending of a string and, if it ends in M-, grep another string that follows it (with junk in between). If the string does not end in M-, then I don't want it copied (let alone any other strings).
So what I would like is:
grep -a -Po "7[[:alnum:]]+(?=M-)" file_name and if the ending is M- then grep -a -Po "5x[[:alnum:]]+(?=\^)" file_name to copy the string that starts with 5x and ends with a ^.
In this example:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
The outcome would be:
7cacscKLrrok9bwC3Z64NTnZ
5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
However, if the ending is not M- (more precisely, if the ending is ^S), then do not try the second grep and do not record anything at all.
In this example:
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZ^SGwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
The outcome would be null (nothing copied) as the 7cacs... string ends in ^S.
Is grep the correct tool? Grep a file and if the condition in the grep command is 'yes' then issue a different grep command but if the condition is 'no' then do nothing.
Thanks again.
I have noticed one addition modification.
Can one add an OR command to the second part? Grep if the second string starts with 5x OR 6x?
In the example below, grep -aPo "7[[:alnum:]]+M-.*?5x[[:alnum:]]+\^" filename | grep -aPo "7[[:alnum:]]+(?=M-)|5x[[:alnum:]]+(?=\^)" will extract the strings starting with 7 and the strings starting with 5x.
How can one change the 5x to 5x or 6x?
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7cacscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
D-wM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM-FM MM-[o#^B^#^#^#^#^#E7AAAAAscKLrrok9bwC3Z64NTnZM-^GwM-^?^#^#^#^#^#^#^#^Y^#^#^#^#^#^#^#M-lM-FM-MM-[o#^B^#M-lM6x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk^89038432nowefe
In this example, the desired outcome would be:
7cacscKLrrok9bwC3Z64NTnZ
5x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
7AAAAAscKLrrok9bwC3Z64NTnZ
6x8w09qewqlkcklwnlkewflewfiewjfoewnflwenfwlkfwelk
UPDATE MARCH 09:
I need to create a series of complex grep (or perl) commands to extract strings from a series of binary files.
I need two strings from the binary file.
The first string will always start with a 1.
The first string will end with a letter or number. The next letter will always be a lower case k. I do not want this k character.
The difficulty is that the ending k will not always be the first k in the string. It might be the first k but it might not.
After the k, there is a second string. The second string will always start with an A or a B.
The ending of the second string will be in one of two forms:
a) it will end with a space then display the first three characters from the first string in lower case followed by a )
b) it will end with a ^K then display the first three characters from the first string in lower case.
For example:
1pppsx9YPar8Rvs75tJYWZq3eo8PgwbckB4m4zT7Yg042KIDYUE82e893hY ppp)
Should be:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc and B4m4zT7Yg042KIDYUE82e893hY - delete the k and the space then ppp.
For example:
1zzzsx9YPkr8Rvs75tJYWZq3eo8PgwbckA2m4zT7Yg042KIDYUE82e893hY^Kzzz
Should be:
1zzzsx9YPkar8Rvs75tJYWZq3eo8Pgwbc and A4m4zT7Yg042KIDYUE82e893hY - delete the second k and the ^Kzzz.
In the second example, we see that the first k is part of the first string. It is the k before the A that breaks up the first and second strings.
I hope there is a super grep expert who can help! Many thanks!
If your grep supports -P option, would you please try:
grep -a -Po "7[[:alnum:]]+(?=M-)" file
The -a option forces grep to read the input as a text file.
The -P option enables the perl-compatible regex.
The -o option tells grep to print only the matched substring(s).
The pattern (?=M-) is a zero-width lookahead assertion (introduced in
Perl) without including it in the result.
Alternatively you can also say with sed:
sed 's/M-/\n/g' file | sed -n 's/.*\(7[[:alnum:]]\+\).*/\1/p'
The first sed command splits the input file into miltiple lines by
replacing the substring M- with a newline.
It has two benefits: it breaks the lines to allow multiple matches with
sed and excludes the unnecessary portion M- from the input.
The next sed command extracts the desired pattern from the input.
It assumes your sed accepts \n in the replacement, which is
a GNU extension (not POSIX compliant). Otherwise please try (in case you are working on bash):
sed 's/M-/\'$'\n''/g' file | sed -n 's/.*\(7[[:alnum:]]\+\).*/\1/p'
[UPDATE]
(The requirement has been updated by the OP and the followings are solutions according to it.)
Let me assume the string which starts with 7 and ends with M- is always followed
by another (no more and no less than one) string which starts with 5x and ends
with ^ (ascii caret character) with junks in between.
Then would you please try the following:
grep -aPo "7[[:alnum:]]+M-.*?5x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|5x[[:alnum:]]+(?=\^)"
It executes the task in two steps (two cascaded greps).
The 1st grep narrows down the input data into the candidate substring
which will include the desired two sequences and junks in between.
The regex .*? in between matches any (ascii or binary) characters
except for a newline character.
The trailing ? enables the shortest match
which avoids the overrun due to the greedy nature of regex. The regex is intended to match junks in between.
The 2nd grep includes two regex's merged with a pipe | meaning logical OR.
Then it extracts two desired sequences.
A potential problem of grep solution is that grep is a line oriented command
and cannot include the newline character in the matched string.
If a newline character is included in the junks in between (I'm not sure about the possibility), the above solution will fail.
As a workaround, perl will provide flexible manipulations with binary data.
perl -0777 -ne '
while (/(7[[:alnum:]]+)M-.*?(5x[[:alnum:]]+)\^/sg) {
printf("%s\n%s\n", $1, $2);
}
' file
The regex is mostly same as that of grep because the -P option of grep means
perl-compatible.
It can capture multiple patterns at once in variables $1 and $2 hence just one regex is enough.
The -0777 option to the perl command tells perl to slurp all data
at once.
The s option at the end the regex makes a dot match a newline character.
The g option enables the global (multiple) match.
[UPDATE2]
In order to make the regex match either 5x or 6x, replace 5x with (5|6)x.
Namely:
grep -aPo "7[[:alnum:]]+M-.*?(5|6)x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|(5|6)x[[:alnum:]]+(?=\^)"
As mentioned before, the pipe | means OR. The OR operator has the lowest priority in the evaluation, hence you need to enclose them with parens in this case.
If there is a possibility any other number than 5 or 6 may appear, it will be safer to put [[:digit:]] instead, which matches any one digit betweeen 0 and 9:
grep -aPo "7[[:alnum:]]+M-.*?[[:digit:]]x[[:alnum:]]+\^" file | grep -aPo "7[[:alnum:]]+(?=M-)|[[:digit:]]x[[:alnum:]]+(?=\^)"
[UPDATE3]
(Answering the OP's requirement on March 9th)
Let me start with a perl code which regex will be relatively easier
to explain.
perl -0777 -ne 'while (/(1(.{3}).+)k([AB].*)[\013 ]\2/g){print "$1 $3\n"}' file
Output:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc B4m4zT7Yg042KIDYUE82e893hY
1zzzsx9YPkr8Rvs75tJYWZq3eo8Pgwbc A2m4zT7Yg042KIDYUE82e893hY
[Explanation of regex]
(1(.{3}).+)k([AB].*)[\013 ]\2
( start of the 1st capture group referred by $1 later
1 literal "1"
( start of the 2nd capture group referred by \2 later
.{3} a sequence of the identical three characters such as ppp or zzz
) end of the 2nd capture group
.+ followed by any characters with "greedy" match which may include the 1st "k"
) end of the 1st capture group
k literal "k"
( start of the 3rd capture group referred by $3 later
[AB].* the character "A" or "B" followed by any characters
) end of the 3rd capture group
[\013 ] followed by ^K or a whitespace
\2 followed by the capture group 2 previously assigned
When implementing it with grep, we will encounter a limitation of grep.
Although we want to extract multiple patterns from the input file,
the -e option (which can specify multiple search patterns) does not
work with -P option. Then we need to split the regex into two patterns
such as:
grep -Po "(1(.{3}).+)(?=k([AB].*)[\013 ]\2)" file
grep -Po "(1(.{3}).+)k\K([AB].*)(?=[\013 ]\2)" file
And the result will be:
1pppsx9YPar8Rvs75tJYWZq3eo8Pgwbc
1zzzsx9YPkr8Rvs75tJYWZq3eo8Pgwbc
B4m4zT7Yg042KIDYUE82e893hY
A2m4zT7Yg042KIDYUE82e893hY
Please be noted the order of output is not same as the order of appearance in the original file.
Another option will be to introduce ripgrep or rg which is a fast
and versatile version of grep. You may need to install ripgrep with
sudo apt install ripgrep or using other package handling tool.
An advantage of ripgrep is it supports -r (replace) option in which
you can make use of the backreferences:
rg -N -Po "(1(.{3}).+)k([AB].*)[\013 ]\2" -r '$1 $3' file
The -r '$1 $3' option prints the 1st and the 3rd capture groups and the result will be the same as perl.
In the general case, you can use the strings utility to pluck out ASCII from binary files; then of course you can try to grep that output for patterns that you find interesting.
Many traditional Unix utilities like grep have internal special markers which might get messed up by binary input. For example, the character \xFF was used for internal purposes by some versions of GNU grep so you can't grep for that character even if you can figure out a way to represent it in the shell (Bash supports $'\xff' for example).
A traditional approach would be to run hexdump or a similar utility, and then grep that for patterns. However, more modern scripting languages like Perl and Python make it easy to manipulate arbitrary binary data.
perl -ne 'print if m/\xff\xff/' </dev/urandom
This might work for you (GNU sed):
sed -En '/\n/!{s/M-\^G/\n/;s/7[^\n]*\n/\n&/};/^7[^\n]*/P;D' file
Split each line into zero or more lines that begin with 7 and end just before M-^G and only print such lines.

How to use sed to search and replace a pattern who appears multiple times in the same line?

Because the question can be misleading, here is a little example. I have this kind of file:
some text
some text ##some-text-KEY-some-other-text##
text again ##some-text-KEY-some-other-text## ##some-text-KEY-some-other-text##
again ##some-text-KEY-some-other-text-KEY-text##
some text with KEY ##KEY-some-text##
blabla ##KEY##
In this example, I want to replace each occurrence of KEY- inside a pair of ## by VALUE-. I started with this sed command:
sed -i 's/\(##[^#]*\)KEY-\([^#]*##\)/\1VALUE-\2/g'
Here is how it works:
\(##[^#]*\): create a first group composed of two # and any characters except # ...
KEY-: ... until the last occurrence of KEY- on that line
\([^#]*##\): and create a second group with all the characters except # until the next pair of #.
The problem is my command can't handle correctly the following line because there are multiple KEY- inside my pair of ##:
again ##some-text-KEY-some-other-text-KEY-text##
Indeed, I get this result:
again ##some-text-KEY-some-other-text-VALUE-text##
If I want to replace all the occurrences of KEY- in that line, I have to run my command multiple times and I prefer to avoid that. I also tried with lazy operators but the problem is the same.
How can I create a regex and a sed command who can handle correctly all my file?
The problem is rather complex: you need to replace all occurrences of some multicharacter text inside blocks of text between identical multicharacter delimiters.
The easiest and safest way to solve the task is using Perl:
perl -i -pe 's/(##)(.*?)(##)/$end_delim=$3; "$1" . $2=~s|KEY-|VALUE-|gr . "$end_delim"/ge' file
See the online demo.
The (##)(.*?)(##) pattern will match strings between two adjacent ## substrings capturing the start delimiter into Group 1, end delimiter in Group 3, and all text in between into Group 2. Since the regex substitution re-sets all placeholders, the temporary variable is used to keep the value of the end delimiter ($end_delim=$3), then, "$1" . $2=~s|KEY-|VALUE-|gr . "$end_delim" replaces the match with the value in the Group 1 of the first match (the first ##), then the Group 2 value with all KEY- replaced with VALUE-, and then the end delimiter.
If there are no KEY-s in between matches on the same line you may use a branch with sed by enclosing your command with :A and tA:
sed -i ':A; s/\(##[^#]*\)KEY-\([^#]*##\)/\1VALUE-\2/g; tA' file
Note you missed the first placeholder in \VALUE-\2, it should be \1VALUE-\2.
See the online demo:
s="some KEY- text
some text ##some-text-KEY-some-other-text##
text again ##some-text-KEY-some-other-text## ##some-text-KEY-some-other-text##
again ##some-text-KEY-some-other-text-KEY-text##
some text with KEY ##KEY-some-text##
blabla ##KEY##"
sed ':A; s/\(##[^#]*\)KEY-\([^#]*##\)/\1VALUE-\2/g; tA' <<< "$s"
Output:
some KEY- text
some text ##some-text-VALUE-some-other-text##
text again ##some-text-VALUE-some-other-text## ##some-text-VALUE-some-other-text##
again ##some-text-VALUE-some-other-text-VALUE-text##
some text with KEY ##VALUE-some-text##
blabla ##KEY##
More details:
sed allows the usage of loops and branches. The :A in the code above is a label, a special location marker that can be "jumped at" using the appropriate operator. t is used to create a branch, this "command jumps to the label only if the previous substitute command was successful". So, once the pattern matched and the replacement occurred, sed goes back to where it was and re-tries a match. If it is not successful, sed goes on to search for the matches further in the string. So, tA means go back to the location marked with A if there was a successful search-and-replace operation.
This might work for you (GNU sed):
sed -E 's/##/\n/g;:a;s/^([^\n]*(\n[^\n]*\n[^\n]*)*\n[^\n]*)KEY-/\1VALUE-/;ta;s/\n/##/g' file
Convert ##'s to newlines. Using a loop, replace VAL- between matched newlines to VALUE-. When all done replace newlines by ##'s.

Regex parsing issue of multi-line file, replacing two consistent patterns around arbitrary persistent text [duplicate]

I'm trying to use sed to clean up lines of URLs to extract just the domain.
So from:
http://www.suepearson.co.uk/product/174/71/3816/
I want:
http://www.suepearson.co.uk/
(either with or without the trailing slash, it doesn't matter)
I have tried:
sed 's|\(http:\/\/.*?\/\).*|\1|'
and (escaping the non-greedy quantifier)
sed 's|\(http:\/\/.*\?\/\).*|\1|'
but I can not seem to get the non-greedy quantifier (?) to work, so it always ends up matching the whole string.
Neither basic nor extended Posix/GNU regex recognizes the non-greedy quantifier; you need a later regex. Fortunately, Perl regex for this context is pretty easy to get:
perl -pe 's|(http://.*?/).*|\1|'
In this specific case, you can get the job done without using a non-greedy regex.
Try this non-greedy regex [^/]* instead of .*?:
sed 's|\(http://[^/]*/\).*|\1|g'
With sed, I usually implement non-greedy search by searching for anything except the separator until the separator :
echo "http://www.suon.co.uk/product/1/7/3/" | sed -n 's;\(http://[^/]*\)/.*;\1;p'
Output:
http://www.suon.co.uk
this is:
don't output -n
search, match pattern, replace and print s/<pattern>/<replace>/p
use ; search command separator instead of / to make it easier to type so s;<pattern>;<replace>;p
remember match between brackets \( ... \), later accessible with \1,\2...
match http://
followed by anything in brackets [], [ab/] would mean either a or b or /
first ^ in [] means not, so followed by anything but the thing in the []
so [^/] means anything except / character
* is to repeat previous group so [^/]* means characters except /.
so far sed -n 's;\(http://[^/]*\) means search and remember http://followed by any characters except / and remember what you've found
we want to search untill the end of domain so stop on the next / so add another / at the end: sed -n 's;\(http://[^/]*\)/' but we want to match the rest of the line after the domain so add .*
now the match remembered in group 1 (\1) is the domain so replace matched line with stuff saved in group \1 and print: sed -n 's;\(http://[^/]*\)/.*;\1;p'
If you want to include backslash after the domain as well, then add one more backslash in the group to remember:
echo "http://www.suon.co.uk/product/1/7/3/" | sed -n 's;\(http://[^/]*/\).*;\1;p'
output:
http://www.suon.co.uk/
Simulating lazy (un-greedy) quantifier in sed
And all other regex flavors!
Finding first occurrence of an expression:
POSIX ERE (using -r option)
Regex:
(EXPRESSION).*|.
Sed:
sed -r ‍'s/(EXPRESSION).*|./\1/g' # Global `g` modifier should be on
Example (finding first sequence of digits) Live demo:
$ sed -r 's/([0-9]+).*|./\1/g' <<< 'foo 12 bar 34'
12
How does it work?
This regex benefits from an alternation |. At each position engine tries to pick the longest match (this is a POSIX standard which is followed by couple of other engines as well) which means it goes with . until a match is found for ([0-9]+).*. But order is important too.
Since global flag is set, engine tries to continue matching character by character up to the end of input string or our target. As soon as the first and only capturing group of left side of alternation is matched (EXPRESSION) rest of line is consumed immediately as well .*. We now hold our value in the first capturing group.
POSIX BRE
Regex:
\(\(\(EXPRESSION\).*\)*.\)*
Sed:
sed 's/\(\(\(EXPRESSION\).*\)*.\)*/\3/'
Example (finding first sequence of digits):
$ sed 's/\(\(\([0-9]\{1,\}\).*\)*.\)*/\3/' <<< 'foo 12 bar 34'
12
This one is like ERE version but with no alternation involved. That's all. At each single position engine tries to match a digit.
If it is found, other following digits are consumed and captured and the rest of line is matched immediately otherwise since * means
more or zero it skips over second capturing group \(\([0-9]\{1,\}\).*\)* and arrives at a dot . to match a single character and this process continues.
Finding first occurrence of a delimited expression:
This approach will match the very first occurrence of a string that is delimited. We can call it a block of string.
sed 's/\(END-DELIMITER-EXPRESSION\).*/\1/; \
s/\(\(START-DELIMITER-EXPRESSION.*\)*.\)*/\1/g'
Input string:
foobar start block #1 end barfoo start block #2 end
-EDE: end
-SDE: start
$ sed 's/\(end\).*/\1/; s/\(\(start.*\)*.\)*/\1/g'
Output:
start block #1 end
First regex \(end\).* matches and captures first end delimiter end and substitues all match with recent captured characters which
is the end delimiter. At this stage our output is: foobar start block #1 end.
Then the result is passed to second regex \(\(start.*\)*.\)* that is same as POSIX BRE version above. It matches a single character
if start delimiter start is not matched otherwise it matches and captures the start delimiter and matches the rest of characters.
Directly answering your question
Using approach #2 (delimited expression) you should select two appropriate expressions:
EDE: [^:/]\/
SDE: http:
Usage:
$ sed 's/\([^:/]\/\).*/\1/g; s/\(\(http:.*\)*.\)*/\1/' <<< 'http://www.suepearson.co.uk/product/174/71/3816/'
Output:
http://www.suepearson.co.uk/
Note: this will not work with identical delimiters.
sed does not support "non greedy" operator.
You have to use "[]" operator to exclude "/" from match.
sed 's,\(http://[^/]*\)/.*,\1,'
P.S. there is no need to backslash "/".
sed - non greedy matching by Christoph Sieghart
The trick to get non greedy matching in sed is to match all characters excluding the one that terminates the match. I know, a no-brainer, but I wasted precious minutes on it and shell scripts should be, after all, quick and easy. So in case somebody else might need it:
Greedy matching
% echo "<b>foo</b>bar" | sed 's/<.*>//g'
bar
Non greedy matching
% echo "<b>foo</b>bar" | sed 's/<[^>]*>//g'
foobar
Non-greedy solution for more than a single character
This thread is really old but I assume people still needs it.
Lets say you want to kill everything till the very first occurrence of HELLO. You cannot say [^HELLO]...
So a nice solution involves two steps, assuming that you can spare a unique word that you are not expecting in the input, say top_sekrit.
In this case we can:
s/HELLO/top_sekrit/ #will only replace the very first occurrence
s/.*top_sekrit// #kill everything till end of the first HELLO
Of course, with a simpler input you could use a smaller word, or maybe even a single character.
HTH!
This can be done using cut:
echo "http://www.suepearson.co.uk/product/174/71/3816/" | cut -d'/' -f1-3
another way, not using regex, is to use fields/delimiter method eg
string="http://www.suepearson.co.uk/product/174/71/3816/"
echo $string | awk -F"/" '{print $1,$2,$3}' OFS="/"
sed certainly has its place but this not not one of them !
As Dee has pointed out: Just use cut. It is far simpler and much more safe in this case. Here's an example where we extract various components from the URL using Bash syntax:
url="http://www.suepearson.co.uk/product/174/71/3816/"
protocol=$(echo "$url" | cut -d':' -f1)
host=$(echo "$url" | cut -d'/' -f3)
urlhost=$(echo "$url" | cut -d'/' -f1-3)
urlpath=$(echo "$url" | cut -d'/' -f4-)
gives you:
protocol = "http"
host = "www.suepearson.co.uk"
urlhost = "http://www.suepearson.co.uk"
urlpath = "product/174/71/3816/"
As you can see this is a lot more flexible approach.
(all credit to Dee)
sed 's|(http:\/\/[^\/]+\/).*|\1|'
There is still hope to solve this using pure (GNU) sed. Despite this is not a generic solution in some cases you can use "loops" to eliminate all the unnecessary parts of the string like this:
sed -r -e ":loop" -e 's|(http://.+)/.*|\1|' -e "t loop"
-r: Use extended regex (for + and unescaped parenthesis)
":loop": Define a new label named "loop"
-e: add commands to sed
"t loop": Jump back to label "loop" if there was a successful substitution
The only problem here is it will also cut the last separator character ('/'), but if you really need it you can still simply put it back after the "loop" finished, just append this additional command at the end of the previous command line:
-e "s,$,/,"
sed -E interprets regular expressions as extended (modern) regular expressions
Update: -E on MacOS X, -r in GNU sed.
Because you specifically stated you're trying to use sed (instead of perl, cut, etc.), try grouping. This circumvents the non-greedy identifier potentially not being recognized. The first group is the protocol (i.e. 'http://', 'https://', 'tcp://', etc). The second group is the domain:
echo "http://www.suon.co.uk/product/1/7/3/" | sed "s|^\(.*//\)\([^/]*\).*$|\1\2|"
If you're not familiar with grouping, start here.
I realize this is an old entry, but someone may find it useful.
As the full domain name may not exceed a total length of 253 characters replace .* with .\{1, 255\}
This is how to robustly do non-greedy matching of multi-character strings using sed. Lets say you want to change every foo...bar to <foo...bar> so for example this input:
$ cat file
ABC foo DEF bar GHI foo KLM bar NOP foo QRS bar TUV
should become this output:
ABC <foo DEF bar> GHI <foo KLM bar> NOP <foo QRS bar> TUV
To do that you convert foo and bar to individual characters and then use the negation of those characters between them:
$ sed 's/#/#A/g; s/{/#B/g; s/}/#C/g; s/foo/{/g; s/bar/}/g; s/{[^{}]*}/<&>/g; s/}/bar/g; s/{/foo/g; s/#C/}/g; s/#B/{/g; s/#A/#/g' file
ABC <foo DEF bar> GHI <foo KLM bar> NOP <foo QRS bar> TUV
In the above:
s/#/#A/g; s/{/#B/g; s/}/#C/g is converting { and } to placeholder strings that cannot exist in the input so those chars then are available to convert foo and bar to.
s/foo/{/g; s/bar/}/g is converting foo and bar to { and } respectively
s/{[^{}]*}/<&>/g is performing the op we want - converting foo...bar to <foo...bar>
s/}/bar/g; s/{/foo/g is converting { and } back to foo and bar.
s/#C/}/g; s/#B/{/g; s/#A/#/g is converting the placeholder strings back to their original characters.
Note that the above does not rely on any particular string not being present in the input as it manufactures such strings in the first step, nor does it care which occurrence of any particular regexp you want to match since you can use {[^{}]*} as many times as necessary in the expression to isolate the actual match you want and/or with seds numeric match operator, e.g. to only replace the 2nd occurrence:
$ sed 's/#/#A/g; s/{/#B/g; s/}/#C/g; s/foo/{/g; s/bar/}/g; s/{[^{}]*}/<&>/2; s/}/bar/g; s/{/foo/g; s/#C/}/g; s/#B/{/g; s/#A/#/g' file
ABC foo DEF bar GHI <foo KLM bar> NOP foo QRS bar TUV
Have not yet seen this answer, so here's how you can do this with vi or vim:
vi -c '%s/\(http:\/\/.\{-}\/\).*/\1/ge | wq' file &>/dev/null
This runs the vi :%s substitution globally (the trailing g), refrains from raising an error if the pattern is not found (e), then saves the resulting changes to disk and quits. The &>/dev/null prevents the GUI from briefly flashing on screen, which can be annoying.
I like using vi sometimes for super complicated regexes, because (1) perl is dead dying, (2) vim has a very advanced regex engine, and (3) I'm already intimately familiar with vi regexes in my day-to-day usage editing documents.
Since PCRE is also tagged here, we could use GNU grep by using non-lazy match in regex .*? which will match first nearest match opposite of .*(which is really greedy and goes till last occurrence of match).
grep -oP '^http[s]?:\/\/.*?/' Input_file
Explanation: using grep's oP options here where -P is responsible for enabling PCRE regex here. In main program of grep mentioning regex which is matching starting http/https followed by :// till next occurrence of / since we have used .*? it will look for first / after (http/https://). It will print matched part only in line.
echo "/home/one/two/three/myfile.txt" | sed 's|\(.*\)/.*|\1|'
don bother, i got it on another forum :)
sed 's|\(http:\/\/www\.[a-z.0-9]*\/\).*|\1| works too
Here is something you can do with a two step approach and awk:
A=http://www.suepearson.co.uk/product/174/71/3816/
echo $A|awk '
{
var=gensub(///,"||",3,$0) ;
sub(/\|\|.*/,"",var);
print var
}'
Output:
http://www.suepearson.co.uk
Hope that helps!
Another sed version:
sed 's|/[:alnum:].*||' file.txt
It matches / followed by an alphanumeric character (so not another forward slash) as well as the rest of characters till the end of the line. Afterwards it replaces it with nothing (ie. deletes it.)
#Daniel H (concerning your comment on andcoz' answer, although long time ago): deleting trailing zeros works with
s,([[:digit:]]\.[[:digit:]]*[1-9])[0]*$,\1,g
it's about clearly defining the matching conditions ...
You should also think about the case where there is no matching delims. Do you want to output the line or not. My examples here do not output anything if there is no match.
You need prefix up to 3rd /, so select two times string of any length not containing / and following / and then string of any length not containing / and then match / following any string and then print selection. This idea works with any single char delims.
echo http://www.suepearson.co.uk/product/174/71/3816/ | \
sed -nr 's,(([^/]*/){2}[^/]*)/.*,\1,p'
Using sed commands you can do fast prefix dropping or delim selection, like:
echo 'aaa #cee: { "foo":" #cee: " }' | \
sed -r 't x;s/ #cee: /\n/;D;:x'
This is lot faster than eating char at a time.
Jump to label if successful match previously. Add \n at / before 1st delim. Remove up to first \n. If \n was added, jump to end and print.
If there is start and end delims, it is just easy to remove end delims until you reach the nth-2 element you want and then do D trick, remove after end delim, jump to delete if no match, remove before start delim and and print. This only works if start/end delims occur in pairs.
echo 'foobar start block #1 end barfoo start block #2 end bazfoo start block #3 end goo start block #4 end faa' | \
sed -r 't x;s/end//;s/end/\n/;D;:x;s/(end).*/\1/;T y;s/.*(start)/\1/;p;:y;d'
If you have access to gnu grep, then can utilize perl regex:
grep -Po '^https?://([^/]+)(?=)' <<< 'http://www.suepearson.co.uk/product/174/71/3816/'
http://www.suepearson.co.uk
Alternatively, to get everything after the domain use
grep -Po '^https?://([^/]+)\K.*' <<< 'http://www.suepearson.co.uk/product/174/71/3816/'
/product/174/71/3816/
The following solution works for matching / working with multiply present (chained; tandem; compound) HTML or other tags. For example, I wanted to edit HTML code to remove <span> tags, that appeared in tandem.
Issue: regular sed regex expressions greedily matched over all the tags from the first to the last.
Solution: non-greedy pattern matching (per discussions elsewhere in this thread; e.g. https://stackoverflow.com/a/46719361/1904943).
Example:
echo '<span>Will</span>This <span>remove</span>will <span>this.</span>remain.' | \
sed 's/<span>[^>]*>//g' ; echo
This will remain.
Explanation:
s/<span> : find <span>
[^>] : followed by anything that is not >
*> : until you find >
//g : replace any such strings present with nothing.
Addendum
I was trying to clean up URLs, but I was running into difficulty matching / excluding a word - href - using the approach above. I briefly looked at negative lookarounds (Regular expression to match a line that doesn't contain a word) but that approach seemed overly complex and did not provide a satisfactory solution.
I decided to replace href with ` (backtick), do the regex substitutions, then replace ` with href.
Example (formatted here for readability):
printf '\n
<a aaa h href="apple">apple</a>
<a bbb "c=ccc" href="banana">banana</a>
<a class="gtm-content-click"
data-vars-link-text="nope"
data-vars-click-url="https://blablabla"
data-vars-event-category="story"
data-vars-sub-category="story"
data-vars-item="in_content_link"
data-vars-link-text
href="https:example.com">Example.com</a>\n\n' |
sed 's/href/`/g ;
s/<a[^`]*`/\n<a href/g'
apple
banana
Example.com
Explanation: basically as above. Here,
s/href/` : replace href with ` (backtick)
s/<a : find start of URL
[^`] : followed by anything that is not ` (backtick)
*` : until you find a `
/<a href/g : replace each of those found with <a href
Unfortunately, as mentioned, this it is not supported in sed.
To overcome this, I suggest to use the next best thing(actually better even), to use vim sed-like capabilities.
define in .bash-profile
vimdo() { vim $2 --not-a-term -c "$1" -es +"w >> /dev/stdout" -cq! ; }
That will create headless vim to execute a command.
Now you can do for example:
echo $PATH | vimdo "%s_\c:[a-zA-Z0-9\\/]\{-}python[a-zA-Z0-9\\/]\{-}:__g" -
to filter out python in $PATH.
Use - to have input from pipe in vimdo.
While most of the syntax is the same. Vim features more advanced features, and using \{-} is standard for non-greedy match. see help regexp.

sed -e "s/^[^#][A-Z]/export /g" will remove first letters... how to prevent this matter?

Say I have this file:
#!/bin/bash
#t1.sh
#There are so many comments here
#I HAVE A PEN
VAR=0
#I GOT AN APPLE
mixed
#APPLE PEN HERE
VAR1=$APPLE_PEN
Now I want to add "export" before every Variable and print result on the screen. I wrote these variable names in upper case then called this sed command:
cat t1.sh|sed -e "s/^[^#][A-Z]/export /g"
But the result removed first letters like:
#I HAVE A PEN
export R1=0
#I GOT AN APPLE
mixed
#APPLE PEN HERE
export R2=$APPLE_PEN
why is that? how to solve it?
BTW,
I could easily make regularexchange on notepad++ on this way:
Will sed also support such exchange too? if so, how to make it?
You need to add a capturing group around the pattern and use a backreference in the RHS part to restore that captured text in the result:
"s/^\([^#][A-Z]\)/export \1/"
^^ ^^ ^^
You need to escape the parentheses since you are using the BRE POSIX regex flavor where an unescaped ( matches a literal open parenthesis.
This might work for you (GNU sed):
sed '/^[^#][A-Z]/s/^/export /' file
Which would read: If the lines first character is not a hash and the second character is a capital letter then insert export followed by a space, at the beginning of the line.
or if you prefer to use a "back reference":
sed 's/^[^#][A-Z]/export &/ file
N.B. there is no need for the g flag on the substitution because when read a line at a time there can only be one start of line.

process a delimited text file with sed

I have a ";" delimited file:
aa;;;;aa
rgg;;;;fdg
aff;sfg;;;fasg
sfaf;sdfas;;;
ASFGF;;;;fasg
QFA;DSGS;;DSFAG;fagf
I'd like to process it replacing the missing value with a \N .
The result should be:
aa;\N;\N;\N;aa
rgg;\N;\N;\N;fdg
aff;sfg;\N;\N;fasg
sfaf;sdfas;\N;\N;\N
ASFGF;\N;\N;\N;fasg
QFA;DSGS;\N;DSFAG;fagf
I'm trying to do it with a sed script:
sed "s/;\(;\)/;\\N\1/g" file1.txt >file2.txt
But what I get is
aa;\N;;\N;aa
rgg;\N;;\N;fdg
aff;sfg;\N;;fasg
sfaf;sdfas;\N;;
ASFGF;\N;;\N;fasg
QFA;DSGS;\N;DSFAG;fagf
You don't need to enclose the second semicolon in parentheses just to use it as \1 in the replacement string. You can use ; in the replacement string:
sed 's/;;/;\\N;/g'
As you noticed, when it finds a pair of semicolons it replaces it with the desired string then skips over it, not reading the second semicolon again and this makes it insert \N after every two semicolons.
A solution is to use positive lookaheads; the regex is /;(?=;)/ but sed doesn't support them.
But it's possible to solve the problem using sed in a simple manner: duplicate the search command; the first command replaces the odd appearances of ;; with ;\N, the second one takes care of the even appearances. The final result is the one you need.
The command is as simple as:
sed 's/;;/;\\N;/g;s/;;/;\\N;/g'
It duplicates the previous command and uses the ; between g and s to separe them. Alternatively you can use the -e command line option once for each search expression:
sed -e 's/;;/;\\N;/g' -e 's/;;/;\\N;/g'
Update:
The OP asks in a comment "What if my file have 100 columns?"
Let's try and see if it works:
$ echo "0;1;;2;;;3;;;;4;;;;;5;;;;;;6;;;;;;;" | sed 's/;;/;\\N;/g;s/;;/;\\N;/g'
0;1;\N;2;\N;\N;3;\N;\N;\N;4;\N;\N;\N;\N;5;\N;\N;\N;\N;\N;6;\N;\N;\N;\N;\N;\N;
Look, ma! It works!
:-)
Update #2
I ignored the fact that the question doesn't ask to replace ;; with something else but to replace the empty/missing values in a file that uses ; to separate the columns. Accordingly, my expression doesn't fix the missing value when it occurs at the beginning or at the end of the line.
As the OP kindly added in a comment, the complete sed command is:
sed 's/;;/;\\N;/g;s/;;/;\\N;/g;s/^;/\\N;/g;s/;$/;\\N/g'
or (for readability):
sed -e 's/;;/;\\N;/g;' -e 's/;;/;\\N;/g;' -e 's/^;/\\N;/g' -e 's/;$/;\\N/g'
The two additional steps replace ';' when they found it at beginning or at the end of line.
You can use this sed command with 2 s (substitute) commands:
sed 's/;;/;\\N;/g; s/;;/;\\N;/g;' file
aa;\N;\N;\N;aa
rgg;\N;\N;\N;fdg
aff;sfg;\N;\N;fasg
sfaf;sdfas;\N;\N;
ASFGF;\N;\N;\N;fasg
QFA;DSGS;\N;DSFAG;fagf
Or using lookarounds regex in a perl command:
perl -pe 's/(?<=;)(?=;)/\\N/g' file
aa;\N;\N;\N;aa
rgg;\N;\N;\N;fdg
aff;sfg;\N;\N;fasg
sfaf;sdfas;\N;\N;
ASFGF;\N;\N;\N;fasg
QFA;DSGS;\N;DSFAG;fagf
The main problem is that you can't use several times the same characters for a single replacement:
s/;;/..../g: The second ; can't be reused for the next match in a string like ;;;
If you want to do it with sed without to use a Perl-like regex mode, you can use a loop with the conditional command t:
sed ':a;s/;;/;\\N;/g;ta;' file
:a defines a label "a", ta go to this label only if something has been replaced.
For the ; at the end of the line (and to deal with eventual trailing whitespaces):
sed ':a;s/;;/;\\N;/g;ta; s/;[ \t\r]*$/;\\N/1' file
this awk one-liner will give you what you want:
awk -F';' -v OFS=';' '{for(i=1;i<=NF;i++)if($i=="")$i="\\N"}7' file
if you really want the line: sfaf;sdfas;\N;\N;\N , this line works for you:
awk -F';' -v OFS=';' '{for(i=1;i<=NF;i++)if($i=="")$i="\\N";sub(/;$/,";\\N")}7' file
sed 's/;/;\\N/g;s/;\\N\([^;]\)/;\1/g;s/;[[:blank:]]*$/;\\N/' YourFile
non recursive, onliner, posix compliant
Concept:
change all ;
put back unmatched one
add the special case of last ; with eventually space before the end of line
This might work for you (GNU sed):
sed -r ':;s/^(;)|(;);|(;)$/\2\3\\N\1\2/g;t' file
There are 4 senarios in which an empty field may occur: at the start of a record, between 2 field delimiters, an empty field following an empty field and at the end of a record. Alternation can be employed to cater for senarios 1,2 and 4 and senario 3 can be catered for by a second pass using a loop (:;...;t). Multiple senarios can be replaced in both passes using the g flag.