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I have a few huge files with values seperated by a pipe (|) sign.
The strings our quoted but sometimes there is a newline in between the quoted string.
I need to read these files with external table from oracle but on the newlines he will give me errors. So I need to replace them with a space.
I do some other perl commands on these files for other errors, so I would like to have a solution in a one line perl command.
I 've found some other similar questions on stackoverflow, but they don't quite do the same and I can't find a solution for my problem with the solution mentioned there.
The statement I tried but that isn't working:
perl -pi -e 's/"(^|)*\n(^|)*"/ /g' test.txt
Sample text:
4454|"test string"|20-05-1999|"test 2nd string"
4455|"test newline
in string"||"test another 2nd string"
4456|"another string"|19-03-2021|"here also a newline
"
4457|.....
Should become:
4454|"test string"|20-05-1999|"test 2nd string"
4455|"test newline in string"||"test another 2nd string"
4456|"another string"|19-03-2021|"here also a newline "
4457|.....
Sounds like you want a CSV parser like Text::CSV_XS (Install through your OS's package manager or favorite CPAN client):
$ perl -MText::CSV_XS -e '
my $csv = Text::CSV_XS->new({sep => "|", binary => 1});
while (my $row = $csv->getline(*ARGV)) {
$csv->say(*STDOUT, [ map { tr/\n/ /r } #$row ])
}' test.txt
4454|"test string"|20-05-1999|"test 2nd string"
4455|"test newline in string"||"test another 2nd string"
4456|"another string"|19-03-2021|"here also a newline "
This one-liner reads each record using | as the field separator instead of the normal comma, and for each field, replaces newlines with spaces, and then prints out the transformed record.
In your specific case, you can also consider a workaround using GNU sed or awk.
An awk command will look like
awk 'NR==1 {print;next;} /^[0-9]{4,}\|/{print "\n" $0;next;}1' ORS="" file > newfile
The ORS (output record separator) is set to an empty string, which means that \n is only added before lines starting with four or more digits followed with a | char (matched with a ^[0-9]{4,}\| POSIX ERE pattern).
A GNU sed command will look like
sed -i ':a;$!{N;/\n[0-9]\{4,\}|/!{s/\n/ /;ba}};P;D' file
This reads two consecutive lines into the pattern space, and once the second line doesn't start with four digits followed with a | char (see the [0-9]\{4\}| POSIX BRE regex pattern), the or more line break between the two is replaced with a space. The search and replace repeats until no match or the end of file.
With perl, if the file is huge but it can still fit into memory, you can use a short
perl -0777 -pi -e 's/\R++(?!\d{4,}\|)/ /g' <<< "$s"
With -0777, you slurp the file and the \R++(?!\d{4,}\|) pattern matches any one or more line breaks (\R++) not followed with four or more digits followed with a | char. The ++ possessive quantifier is required to make (?!...) negative lookahead to disallow backtracking into line break matching pattern.
With your shown samples, this could be simply done in awk program. Written and tested in GNU awk, should work in any awk. This should work fast even on huge files(better than slurping whole file into memory, having mentioned that OP may use it on huge files).
awk 'gsub(/"/,"&")%2!=0{if(val==""){val=$0} else{print val $0;val=""};next} 1' Input_file
Explanation: Adding detailed explanation for above.
awk ' ##Starting awk program from here.
gsub(/"/,"&")%2!=0{ ##Checking condition if number of " are EVEN or not, because if they are NOT even then it means they are NOT closed properly.
if(val==""){ val=$0 } ##Checking condition if val is NULL then set val to current line.
else {print val $0;val=""} ##Else(if val NOT NULL) then print val current line and nullify val here.
next ##next will skip further statements from here.
}
1 ##In case number of " are EVEN in any line it will skip above condition(gusb one) and simply print the line.
' Input_file ##Mentioning Input_file name here.
I've scraped a large amount (10GB) of PDFs and converted them to text files, but due to the format of the original PDFs, there is an issue:
Many of the words which break across lines have a dash in them that artificially breaks up the word, like this:
You can see that this happened because the original PDFs files have breaks:
What would be the cleanest and fastest way to "join" every word instance that matches this pattern inside of a .txt file?
Perhaps some sort of Regex search, like for a [a-z]\-\s \w of some kind (word character followed by dash followed by space) would work?
Or would some sort of sed replacement work better?
Currently, I'm trying to get a sed regex to work, but I'm not sure how to translate this to use capture groups to replace the selected text:
sed -n '\%\w\- [a-z]%p' Filename.txt
My input text would look like this:
The dog rolled down the st- eep hill and pl- ayed outside.
And the output would be:
The dog rolled down the steep hill and played outside.
Ideally, the expression would also work for words split up by a newline, like this:
The rule which provided for the consid-
eration of the resolution, was agreed to earlier by a
To this:
The rule which provided for the consideration
of the resolution, was agreed to earlier by a
It's straightforward in sed:
sed -e ':a' -e '/-$/{N;s/-\n//;ba
}' -e 's/- //g' filename
This translates roughly as "if the line ends with a dash, read in the next line as well (so that you have a line with a carriage return in the middle) then excise the dash and carriage return, and loop back the beginning just in case this new line also ends with a dash. Then remove any instances of - ".
You may use this gnu-awk code:
cat file
The dog rolled down the st- eep hill and pl- ayed outside.
The rule which provided for the consid-
eration of the resolution, was agreed to earlier by a
Then use awk like this:
awk 'p != "" {
w = $1
$1 = ""
sub(/^[[:blank:]]+/, ORS)
$0 = p w $0
p = ""
}
{
$0 = gensub(/([_[:alnum:]])-[[:blank:]]+([_[:alnum:]])/, "\\1\\2", "g")
}
/-$/ {
p = $0
sub(/-$/, "", p)
}
p == ""' file
The dog rolled down the steep hill and played outside.
The rule which provided for the consideration
of the resolution, was agreed to earlier by a
If you can consider perl then this may also work for you:
Then use:
perl -0777 -pe 's/(\w)-\h+(\w)/$1$2/g; s/(\w)-\R(\w+)\s+/$1$2\n/g' file
You simply add backslash-parentheses (or use the -r or -E option if available to do away with the requirement to put backslashes before capturing parentheses) and recall the matched text with \1 for the first capturing parenthesis, \2 for the second, etc.
sed 's/\(\w\)\- \([a-z]\)/\1\2/g' Filename.txt
The \w escape is not standard sed but if it works for you, feel free to use it. Otherwise, it is easy to replace with [A-Za-z0-9_#] or whatever else you want to call "word characters".
I'm guessing not all of the matches will be hyphenated words so perhaps run the result through a spelling checker or something to verify whether the result is an English word. (I would probably switch to a more capable scripting language like Python for that, though.)
I have the next strings:
for example:
input1 = abc-def-ghi-jkl
input2 = mno-pqr-stu-vwy
I want extract the first word between "-"
for the fisrt string I want to get: def
if the input is the second string, I want to get: pqr
I want to use the command SED, Could you help me please?
Use
sed 's,^[^-]*-\([^-]*\).*,\1,' file
The string after the first - will be captured up to the second - and the rest will be matched, then the matched line will be replaced with the group text.
With bash:
var='input1 = abc-def-ghi-jkl'
var=${var#*-} # remove shortest prefix `*-`, this removes `input1 = abc-`
echo "${var%%-*}" # remove longest suffix `-*`, this removes `-ghi-jkl`
Or with awk:
awk -F'-' '{print $2}' <<<'input1 = abc-def-ghi-jkl'
Use - as input field separator and print the second field.
Or with cut:
cut -d'-' -f2 <<<'input1 = abc-def-ghi-jkl'
When you want to use sed, you can choose between solutions like
# Double processing
echo "$input1" | sed 's/[^-]*-//;s/-.*//'
# Normal approach
echo "$input1" | sed -r 's/^[^-]*-([^-]*)|-.*)/\1/g'
# Funny alternative
echo "$input1" | sed -r 's/(^[^-]*-|-.*)//g'
The obvious "external" tool would be cut. You can also look at a Bash builtin solution like
[[ ${input1} =~ ([^-]*)-([^-]*) ]] && printf %s "${BASH_REMATCH[2]}"
grep solution (in my opinion this is the most natural approach, as you are only trying to find matches to a regular expression - you are not looking to edit anything, so there should be no need for the more advanced command sed)
grep -oP '^[^-]*-\K[^-]*(?=-)' << EOF
> abc-qrs-bobo-the-clown
> 123-45-6789
> blah-blah-blah
> no dashes here
> mahi-mahi
> EOF
Output
qrs
45
blah
Explanation
Look at the inputs first, included here for completeness as a heredoc (more likely you would name your file as the last argument to grep.) The solution requires at least two dashes to be present in the string; in particular, for mahi-mahi it will find no match. If you want to find the second mahi as a match, you can remove the lookahead assertion at the end of the regular expression (see below).
The regular expression does this. First note the command options: -o to return only the matched substring, not the entire line; and -P to use Perl extensions. Then, the regular expression: start from the beginning of the line (^); look for zero or more non-dash characters followed by dash, and then (\K) discard this part of the required match from the substrings found to match the pattern. Then look for zero or more non-dash characters again - this will be returned by the command. Finally, require a dash following this pattern, but do not include it in the match. This is done with a lookahead (marked by (?= ... )).
How do I remove duplicate characters and keep the unique one only.
For example, my input is:
EFUAHUU
UUUEUUUUH
UJUJHHACDEFUCU
Expected output is:
EFUAH
UEH
UJHACDEF
I came across perl -pe's/$1//g while/(.).*\/' which is wonderful but it is removing even the single occurrence of the character in output.
This can be done using positive lookahead :
perl -pe 's/(.)(?=.*?\1)//g' FILE_NAME
The regex used is: (.)(?=.*?\1)
. : to match any char.
first () : remember the matched
single char.
(?=...) : +ve lookahead
.*? : to match anything in between
\1 : the remembered match.
(.)(?=.*?\1) : match and remember
any char only if it appears again
later in the string.
s/// : Perl way of doing the
substitution.
g: to do the substitution
globally...that is don't stop after
first substitution.
s/(.)(?=.*?\1)//g : this will
delete a char from the input string
only if that char appears again later
in the string.
This will not maintain the order of the char in the input because for every unique char in the input string, we retain its last occurrence and not the first.
To keep the relative order intact we can do what KennyTM tells in one of the comments:
reverse the input line
do the substitution as before
reverse the result before printing
The Perl one line for this is:
perl -ne '$_=reverse;s/(.)(?=.*?\1)//g;print scalar reverse;' FILE_NAME
Since we are doing print manually after reversal, we don't use the -p flag but use the -n flag.
I'm not sure if this is the best one-liner to do this. I welcome others to edit this answer if they have a better alternative.
if Perl is not a must, you can also use awk. here's a fun benchmark on the Perl one liners posted against awk. awk is 10+ seconds faster for a file with 3million++ lines
$ wc -l <file2
3210220
$ time awk 'BEGIN{FS=""}{delete _;for(i=1;i<=NF;i++){if(!_[$i]++) printf $i};print""}' file2 >/dev/null
real 1m1.761s
user 0m58.565s
sys 0m1.568s
$ time perl -n -e '%seen=();' -e 'for (split //) {print unless $seen{$_}++;}' file2 > /dev/null
real 1m32.123s
user 1m23.623s
sys 0m3.450s
$ time perl -ne '$_=reverse;s/(.)(?=.*?\1)//g;print scalar reverse;' file2 >/dev/null
real 1m17.818s
user 1m10.611s
sys 0m2.557s
$ time perl -ne'my%s;print grep!$s{$_}++,split//' file2 >/dev/null
real 1m20.347s
user 1m13.069s
sys 0m2.896s
perl -ne'my%s;print grep!$s{$_}++,split//'
Here is a solution, that I think should work faster than the lookahead one, but is not regexp-based and uses hashtable.
perl -n -e '%seen=();' -e 'for (split //) {print unless $seen{$_}++;}'
It splits every line into characters and prints only the first appearance by counting appearances inside %seen hashtable
Tie::IxHash is a good module to store hash order (but may be slow, you will need to benchmark if speed is important). Example with tests:
use Test::More 0.88;
use Tie::IxHash;
sub dedupe {
my $str=shift;
my $hash=Tie::IxHash->new(map { $_ => 1} split //,$str);
return join('',$hash->Keys);
}
{
my $str='EFUAHUU';
is(dedupe($str),'EFUAH');
}
{
my $str='EFUAHHUU';
is(dedupe($str),'EFUAH');
}
{
my $str='UJUJHHACDEFUCU';
is(dedupe($str),'UJHACDEF');
}
done_testing();
Use uniq from List::MoreUtils:
perl -MList::MoreUtils=uniq -ne 'print uniq split ""'
If the set of characters that can be encountered is restricted, e.g. only letters, then the easiest solution will be with tr
perl -p -e 'tr/a-zA-Z/a-zA-Z/s'
It will replace all the letters by themselves, leaving other characters unaffected and /s modifier will squeeze repeated occurrences of the same character (after replacement), thus removing duplicates
Me bad - it removes only adjoining appearances. Disregard
This looks like a classic application of positive lookbehind, but unfortunately perl doesn't support that. In fact, doing this (matching the preceding text of a character in a string with a full regex whose length is indeterminable) can only be done with .NET regex classes, I think.
However, positive lookahead supports full regexes, so all you need to do is reverse the string, apply positive lookahead (like unicornaddict said):
perl -pe 's/(.)(?=.*?\1)//g'
And reverse it back, because without the reverse that'll only keep the duplicate character at the last place in a line.
MASSIVE EDIT
I've been spending the last half an hour on this, and this looks like this works, without the reversing.
perl -pe 's/\G$1//g while (/(.).*(?=\1)/g)' FILE_NAME
I don't know whether to be proud or horrified. I'm basically doing the positive looakahead, then substituting on the string with \G specified - which makes the regex engine start its matching from the last place matched (internally represented by the pos() variable).
With test input like this:
aabbbcbbccbabb
EFAUUUUH
ABCBBBBD
DEEEFEGGH
AABBCC
The output is like this:
abc
EFAUH
ABCD
DEFGH
ABC
I think it's working...
Explanation - Okay, in case my explanation last time wasn't clear enough - the lookahead will go and stop at the last match of a duplicate variable [in the code you can do a print pos(); inside the loop to check] and the s/\G//g will remove it [you don't need the /g really]. So within the loop, the substitution will continue removing until all such duplicates are zapped. Of course, this might be a little too processor intensive for your tastes... but so are most of the regex-based solutions you'll see. The reversing/lookahead method will probably be more efficient than this, though.
From the shell, this works:
sed -e 's/$/<EOL>/ ; s/./&\n/g' test.txt | uniq | sed -e :a -e '$!N; s/\n//; ta ; s/<EOL>/\n/g'
In words: mark every linebreak with a <EOL> string, then put every character on a line of its own, then use uniq to remove duplicate lines, then strip out all the linebreaks, then put back linebreaks instead of the <EOL> markers.
I found the -e :a -e '$!N; s/\n//; ta part in a forum post and I don't understand the seperate -e :a part, or the $!N part, so if anyone can explain those, I'd be grateful.
Hmm, that one does only consecutive duplicates; to eliminate all duplicates you could do this:
cat test.txt | while read line ; do echo $line | sed -e 's/./&\n/g' | sort | uniq | sed -e :a -e '$!N; s/\n//; ta' ; done
That puts the characters in each line in alphabetical order though.
use strict;
use warnings;
my ($uniq, $seq, #result);
$uniq ='';
sub uniq {
$seq = shift;
for (split'',$seq) {
$uniq .=$_ unless $uniq =~ /$_/;
}
push #result,$uniq;
$uniq='';
}
while(<DATA>){
uniq($_);
}
print #result;
__DATA__
EFUAHUU
UUUEUUUUH
UJUJHHACDEFUCU
The output:
EFUAH
UEH
UJHACDEF
for a file containing the data you list named foo.txt
python -c "print set(open('foo.txt').read())"
I see lots of examples and man pages on how to do things like search-and-replace using sed, awk, or gawk.
But in my case, I have a regular expression that I want to run against a text file to extract a specific value. I don't want to do search-and-replace. This is being called from bash. Let's use an example:
Example regular expression:
.*abc([0-9]+)xyz.*
Example input file:
a
b
c
abc12345xyz
a
b
c
As simple as this sounds, I cannot figure out how to call sed/awk/gawk correctly. What I was hoping to do, is from within my bash script have:
myvalue=$( sed <...something...> input.txt )
Things I've tried include:
sed -e 's/.*([0-9]).*/\\1/g' example.txt # extracts the entire input file
sed -n 's/.*([0-9]).*/\\1/g' example.txt # extracts nothing
My sed (Mac OS X) didn't work with +. I tried * instead and I added p tag for printing match:
sed -n 's/^.*abc\([0-9]*\)xyz.*$/\1/p' example.txt
For matching at least one numeric character without +, I would use:
sed -n 's/^.*abc\([0-9][0-9]*\)xyz.*$/\1/p' example.txt
You can use sed to do this
sed -rn 's/.*abc([0-9]+)xyz.*/\1/gp'
-n don't print the resulting line
-r this makes it so you don't have the escape the capture group parens().
\1 the capture group match
/g global match
/p print the result
I wrote a tool for myself that makes this easier
rip 'abc(\d+)xyz' '$1'
I use perl to make this easier for myself. e.g.
perl -ne 'print $1 if /.*abc([0-9]+)xyz.*/'
This runs Perl, the -n option instructs Perl to read in one line at a time from STDIN and execute the code. The -e option specifies the instruction to run.
The instruction runs a regexp on the line read, and if it matches prints out the contents of the first set of bracks ($1).
You can do this will multiple file names on the end also. e.g.
perl -ne 'print $1 if /.*abc([0-9]+)xyz.*/' example1.txt example2.txt
If your version of grep supports it you could use the -o option to print only the portion of any line that matches your regexp.
If not then here's the best sed I could come up with:
sed -e '/[0-9]/!d' -e 's/^[^0-9]*//' -e 's/[^0-9]*$//'
... which deletes/skips with no digits and, for the remaining lines, removes all leading and trailing non-digit characters. (I'm only guessing that your intention is to extract the number from each line that contains one).
The problem with something like:
sed -e 's/.*\([0-9]*\).*/&/'
.... or
sed -e 's/.*\([0-9]*\).*/\1/'
... is that sed only supports "greedy" match ... so the first .* will match the rest of the line. Unless we can use a negated character class to achieve a non-greedy match ... or a version of sed with Perl-compatible or other extensions to its regexes, we can't extract a precise pattern match from with the pattern space (a line).
You can use awk with match() to access the captured group:
$ awk 'match($0, /abc([0-9]+)xyz/, matches) {print matches[1]}' file
12345
This tries to match the pattern abc[0-9]+xyz. If it does so, it stores its slices in the array matches, whose first item is the block [0-9]+. Since match() returns the character position, or index, of where that substring begins (1, if it starts at the beginning of string), it triggers the print action.
With grep you can use a look-behind and look-ahead:
$ grep -oP '(?<=abc)[0-9]+(?=xyz)' file
12345
$ grep -oP 'abc\K[0-9]+(?=xyz)' file
12345
This checks the pattern [0-9]+ when it occurs within abc and xyz and just prints the digits.
perl is the cleanest syntax, but if you don't have perl (not always there, I understand), then the only way to use gawk and components of a regex is to use the gensub feature.
gawk '/abc[0-9]+xyz/ { print gensub(/.*([0-9]+).*/,"\\1","g"); }' < file
output of the sample input file will be
12345
Note: gensub replaces the entire regex (between the //), so you need to put the .* before and after the ([0-9]+) to get rid of text before and after the number in the substitution.
If you want to select lines then strip out the bits you don't want:
egrep 'abc[0-9]+xyz' inputFile | sed -e 's/^.*abc//' -e 's/xyz.*$//'
It basically selects the lines you want with egrep and then uses sed to strip off the bits before and after the number.
You can see this in action here:
pax> echo 'a
b
c
abc12345xyz
a
b
c' | egrep 'abc[0-9]+xyz' | sed -e 's/^.*abc//' -e 's/xyz.*$//'
12345
pax>
Update: obviously if you actual situation is more complex, the REs will need to me modified. For example if you always had a single number buried within zero or more non-numerics at the start and end:
egrep '[^0-9]*[0-9]+[^0-9]*$' inputFile | sed -e 's/^[^0-9]*//' -e 's/[^0-9]*$//'
The OP's case doesn't specify that there can be multiple matches on a single line, but for the Google traffic, I'll add an example for that too.
Since the OP's need is to extract a group from a pattern, using grep -o will require 2 passes. But, I still find this the most intuitive way to get the job done.
$ cat > example.txt <<TXT
a
b
c
abc12345xyz
a
abc23451xyz asdf abc34512xyz
c
TXT
$ cat example.txt | grep -oE 'abc([0-9]+)xyz'
abc12345xyz
abc23451xyz
abc34512xyz
$ cat example.txt | grep -oE 'abc([0-9]+)xyz' | grep -oE '[0-9]+'
12345
23451
34512
Since processor time is basically free but human readability is priceless, I tend to refactor my code based on the question, "a year from now, what am I going to think this does?" In fact, for code that I intend to share publicly or with my team, I'll even open man grep to figure out what the long options are and substitute those. Like so: grep --only-matching --extended-regexp
why even need match group
gawk/mawk/mawk2 'BEGIN{ FS="(^.*abc|xyz.*$)" } ($2 ~ /^[0-9]+$/) {print $2}'
Let FS collect away both ends of the line.
If $2, the leftover not swallowed by FS, doesn't contain non-numeric characters, that's your answer to print out.
If you're extra cautious, confirm length of $1 and $3 both being zero.
** edited answer after realizing zero length $2 will trip up my previous solution
there's a standard piece of code from awk channel called "FindAllMatches" but it's still very manual, literally, just long loops of while(), match(), substr(), more substr(), then rinse and repeat.
If you're looking for ideas on how to obtain just the matched pieces, but upon a complex regex that matches multiple times each line, or none at all, try this :
mawk/mawk2/gawk 'BEGIN { srand(); for(x = 0; x < 128; x++ ) {
alnumstr = sprintf("%s%c", alnumstr , x)
};
gsub(/[^[:alnum:]_=]+|[AEIOUaeiou]+/, "", alnumstr)
# resulting str should be 44-chars long :
# all digits, non-vowels, equal sign =, and underscore _
x = 10; do { nonceFS = nonceFS substr(alnumstr, 1 + int(44*rand()), 1)
} while ( --x ); # you can pick any level of precision you need.
# 10 chars randomly among the set is approx. 54-bits
#
# i prefer this set over all ASCII being these
# just about never require escaping
# feel free to skip the _ or = or r/t/b/v/f/0 if you're concerned.
#
# now you've made a random nonce that can be
# inserted right in the middle of just about ANYTHING
# -- ASCII, Unicode, binary data -- (1) which will always fully
# print out, (2) has extremely low chance of actually
# appearing inside any real word data, and (3) even lower chance
# it accidentally alters the meaning of the underlying data.
# (so intentionally leaving them in there and
# passing it along unix pipes remains quite harmless)
#
# this is essentially the lazy man's approach to making nonces
# that kinda-sorta have some resemblance to base64
# encoded, without having to write such a module (unless u have
# one for awk handy)
regex1 = (..); # build whatever regex you want here
FS = OFS = nonceFS;
} $0 ~ regex1 {
gsub(regex1, nonceFS "&" nonceFS); $0 = $0;
# now you've essentially replicated what gawk patsplit( ) does,
# or gawk's split(..., seps) tracking 2 arrays one for the data
# in between, and one for the seps.
#
# via this method, that can all be done upon the entire $0,
# without any of the hassle (and slow downs) of
# reading from associatively-hashed arrays,
#
# simply print out all your even numbered columns
# those will be the parts of "just the match"
if you also run another OFS = ""; $1 = $1; , now instead of needing 4-argument split() or patsplit(), both of which being gawk specific to see what the regex seps were, now the entire $0's fields are in data1-sep1-data2-sep2-.... pattern, ..... all while $0 will look EXACTLY the same as when you first read in the line. a straight up print will be byte-for-byte identical to immediately printing upon reading.
Once i tested it to the extreme using a regex that represents valid UTF8 characters on this. Took maybe 30 seconds or so for mawk2 to process a 167MB text file with plenty of CJK unicode all over, all read in at once into $0, and crank this split logic, resulting in NF of around 175,000,000, and each field being 1-single character of either ASCII or multi-byte UTF8 Unicode.
you can do it with the shell
while read -r line
do
case "$line" in
*abc*[0-9]*xyz* )
t="${line##abc}"
echo "num is ${t%%xyz}";;
esac
done <"file"
For awk. I would use the following script:
/.*abc([0-9]+)xyz.*/ {
print $0;
next;
}
{
/* default, do nothing */
}
gawk '/.*abc([0-9]+)xyz.*/' file