I have several (JSON) files in a directory. I am wanting to scan all files for the line with the audio property (first string in quotes) and replace all non-alphanumeric characters in the associated value (second string with quotes) with an underscore. For example, if the line is:
"audio": "Sub Dir/my file` nāme.mp3"
I would like to replace it with:
"audio": "Sub_Dir/my_file__n_me.mp3"
What can I do to replace these lines in multiple files?
If perl is your option, would you please try:
perl -i".bak" -pe 's/("audio":\s"*)(.+?)"/
$x = $1;
($y = $2) =~ s#[^A-Za-z0-9_\/\.]#_#g;
$x . $y . "\""/e' *.json
The e option to the s/../../ function enables the substitution
to be the result of evaluation of perl expression.
The substition s#[^A-Za-z0-9_\/\.]#_#g is performed on the
second string with quotes and replaces characters other
than ascii alphabets, digits, underscores, slashes, dots with underscores.
Original files are saved with the suffix .bak.
Related
I have key value pairs in a string like this:
key1 = "value1"
key2 = "value2"
key3 = "value3"
In a bash script, I need to extract the value of one of the keys like for key2, I should get value2, not in quote.
My bash script needs to work in both Redhat and Ubuntu Linux hosts.
What would be the easiest and most reliable way of doing this?
I tried something like this simplified script:
pattern='key2\s*=\s*\"(.*?)\".*$'
if [[ "$content" =~ $pattern ]]
then
key2="${BASH_REMATCH[1]}"
echo "key2: $key2"
else
echo 'not found'
fi
But it does not work consistently.
Any better/easier/more reliable way of doing this?
To separate the key and value from your $content variable, you can use:
[[ $content =~ (^[^ ]+)[[:blank:]]*=[[:blank:]]*[[:punct:]](.*)[[:punct:]]$ ]]
That will properly populate the BASH_REMATCH array with both values where your key is in BASH_REMATCH[1] and the value in BASH_REMATCH[2].
Explanation
In bash the [[...]] treats what appears on the right side of =~ as an extended regular expression and matched according to man 3 regex. See man 1 bash under the section heading for [[ expression ]] (4th paragraph). Sub-expressions in parenthesis (..) are saved in the array variable BASH_REMATCH with BASH_REMATCH[0] containing the entire portion of the string (your $content) and each remaining elements containing the sub-expressions enclosed in (..) in the order the parenthesis appear in the regex.
The Regular Expression (^[^ ]+)[[:blank:]]*=[[:blank:]]*[[:punct:]](.*)[[:punct:]]$ is explained as:
(^[^ ]+) - '^' anchored at the beginning of the line, [^ ]+ match one or more characters that are not a space. Since this sub-expression is enclosed in (..) it will be saved as BASH_REMATCH[1], followed by;
[[:blank:]]* - zero or more whitespace characters, followed by;
= - an equal sign, followed by;
[[:blank:]]* - zero or more whitespace characters, followed by;
[[:punct:]] - a punctuation character (matching the '"', which avoids caveats associated with using quotes within the regex), followed by the sub-expression;
(.*) - zero or more characters (the rest of the characters), and since it is a sub-expression in (..) it the characters will be stored in BASH_REMATCH[2], followed by;
[[:punct:]] - a punctuation character (matching the '"' ... ditto), at the;
$ - end of line anchor.
So if you match what your key and value input lines separated by an = sign, it will separate the key and value into the array BASH_REMATCH as you wanted.
Bash supports BRE only and you cannot use \s and .*?.
As an alternative, please try:
while IFS= read -r content; do
# pattern='key2\s*=\s*\"(.*)\".*$'
pattern='key2[[:blank:]]*=[[:blank:]]*"([^"]*)"'
if [[ $content =~ $pattern ]]
then
key2="${BASH_REMATCH[1]}"
echo "key2: $key2"
(( found++ ))
fi
done < input-file.txt
if (( found == 0 )); then
echo "not found"
fi
What you start talking about key-value pairs, it is best to use an associative array:
declare -A map
Now looking at your lines, they look like key = "value" where we assume that:
value is always encapsulated by double quotes, but also could contain a quote
an unknown number of white spaces is before and/or after the equal sign.
So assuming we have a variable line which contains key = "value", the following operations will extract that value:
key="${line%%=*}"; key="${key// /}"
value="${line#*=}"; value="${value#*\042}"; value="${value%\042*}"
IFS=" \t=" read -r value _ <<<"$line"
This allows us now to have something like:
declare -A map
while read -r line; do
key="${line%%=*}"; key="${key// /}"
value="${line#*=}"; value="${value#*\042}"; value="${value%\042*}"
map["$key"]="$value"
done <inputfile
With awk:
awk -v key="key2" '$1 == key { gsub("\"","",$3);print $3 }' <<< "$string"
Reading the output of the variable called string, pass the required key in as a variable called key and then if the first space delimited field is equal to the key, remove the quotes from the third field with the gsub function and print.
Ok, after spending so many hours, this is how I solved the problem:
If you don't know where your script will run and what type of file (win/mac/linux) are you reading:
Try to avoid non-greedy macth in linux bash instead of tweaking diffrent switches.
don't trus end of line match $ when you might get data from windows or mac
This post solved my problem: Non greedy text matching and extrapolating in bash
This pattern works for me in may linux environments and all type of end of lines:
pattern='key2\s*=\s*"([^"]*)"'
The value is in BASH_REMATCH[1]
Here is a script I use:
for dir in $(find . -type d -name "single_copy_busco_sequences"); do
sppname=$(dirname $(dirname $(dirname $dir))| sed 's#./##g');
for file in ${dir}/*.faa; do name=$(basename $file); cp $file /Users/admin/Documents/busco_aa/${sppname}_${name}; sed -i '' 's#>#>'${sppname}'|#g' /Users/admin/Documents/busco_aa/${sppname}_${name}; cut -f 1 -d ":" /Users/admin/Documents/busco_aa/${sppname}_${name} > /Users/admin/Documents/busco_aa/${sppname}_${name}.1;
done;
done
The sppname variable is something like Gender_species
do you know how could I add a line in my script to creat a new variable called abbrev which transformes Gender_species into Genspe, the 3 first letters cat with the 3 first letters after _
exemples:
Homo_sapiens gives Homsap
Canis_lupus gives Canlup
etc
Thank for your help :)
You can achieve this using a regular expression with sed:
echo "Homo_sapiens" | sed -e s'/^\(...\).*_\(...\).*/\1\2/'
Homsap
start, get 3 chars (to keep in \1), anything, _, anything, get 3 chars (to keep in \2), anything
Replace echo "Homo_sapiens" by your $dir thing
PS: will fail if you have less than 3 chars in one word
You can do it all with bash built-in parameter expansions. Specifically, string indexes and substring removal.
$ a=Homo_sapiens; prefix=${a:0:3}; a=${a#*_}; postfix=${a:0:3}; echo $prefix$postfix
Homsap
$ a=Canis_lupus; prefix=${a:0:3}; a=${a#*_}; postfix=${a:0:3}; echo $prefix$postfix
Canlup
Using bash built-ins is always more efficient than spawning separate subshell(s) to invoke utilities to accomplish the same thing.
Explanation
Your string index form (bash only) allows you to index characters from within a string, e.g.
* ${parameter:offset:length} ## indexes are zero based, ${a:0:2} is 1st 2 chars
Where parameter is simply the variable name holding the string.
(you can index from the end of a string by using a negative offset preceded by a space or enclosed in parenthesis, e.g. a=12345; echo ${a: -3:2} outputs "34")
prefix=${a:0:3} ## save the first 3 characters in prefix
a=${a#*_} ## remove the front of the string through '_' (see below)
postfix=${a:0:3} ## save the first 3 characters after '_'
Your substring removal forms (POSIX) are:
${parameter#word} trim to 1st occurrence of word from parameter from left
${parameter##word} trim to last occurrence of word from parameter from left
and
${parameter%word} trim to 1st occurrence of word from parameter from right
${parameter%%word} trim to last occurrence of word from parameter from right
(word can contain globbing to expand to a pattern as well)
a=${a#*_} ## trim from left up to (and including) the first '_'
See bash(1) - Linux manual page for full details.
I need to split a string into an array in bash. However, not by a fixed delimiter character, but by a regular expression. Here are the details:
I have a CSV file containing millions of lines of the following format:
123,"usrlogin1","usrname2","companyname1","email#example.com","1970-01-01 00:00:00","USR",0,1
However, some fields may contain escaped quotation marks \" and commas within strings, so a line might just as well look like this:
123,"usrlogin1","usrname2","The \"awesome\" company, NA","email#example.com","1970-01-01 00:00:00","USR",0,1
I need to split this file by the correct commas, that is to say those which are outside of non-escaped quotation marks.
Desired output:
123
usrlogin1
usrname2
The "awesome" company, NA
email#example.com
1970-01-01 00:00:00
USR
0
1
This is where I am at:
#!/bin/sh
#read file line by line
while IFS='' read -r line; do
#replace escaped quotation marks (\") with (")
line=$(echo $line | sed 's/\\"/\"\;/g')
#split this line now by commas
#TODO
done < "$1"
At the point of TODO, I would like to use the following regex as delimiter for splitting my string into an array:
(?!\B"[^"]*),(?![^"]*"\B)
Demo: https://regex101.com/r/xB7rQ7/1
How can I split the $line by the regex above?
So i have an alphanumeric string 10006cc2190ab011 i am trying to add a colon after every two letters in this alphanumeric string.
this is the string : 10006cc2190ab011
i want it be - 10:00:6c:c2:19:0a:b0:11
Thanks in advance.
A sed solution:
$ echo 10006cc2190ab011 | sed 's/../&:/g; s/:$//'
10:00:6c:c2:19:0a:b0:11
Replaces each non-overlapping pair of characters with the same pair plus :. In the end removes the trailing : (if input text had even length).
str=10006cc2190ab011; str="${str//??/${.sh.match}:}"; echo ${str%:}
is doing the same replacement without the use of an external command, just using ksh-internals.
Doing the same as in sed (the other answer). Replace in $str every // two charactes ?? with / the matched string and a : (every match is kept in the ksh-variable ${.sh.match}). Then print $str without the last % ':'.
I'm reading in values from an .ini file, and sometimes may get trailing or leading whitespace.
How do I amend this first line to prevent that?
db=$(sed -n 's/.*DB_USERNAME *= *\([^ ]*.*\)/\1/p' < config.ini);
echo -"$db"-
Result;
-myinivar -
I need;
-myinivar-
Use parameter expansion.
echo "=${db% }="
You don't need the .* inside the capturing group (or the semicolon at the end of line):
db="$(sed -n 's/.*DB_USERNAME *= *\([^ ]*\).*/\1/p' < config.ini)"
To elaborate:
.* matches anything at all
DB_USERNAME matches that literal string
* (a single space followed by an asterisk) matches any number of spaces
= matches that literal string
* (a single space followed by an asterisk) matches any number of spaces
\( starts the capturing group that is used for \1 later
[^ ] matches anything which is not a space character
* repeats that zero or more times
\) ends the capturing group
.* matches anything at all
Therefore, the result will be all the characters after DB_USERNAME = and any number of spaces, up to the next space or end of line, whichever comes first.
You can use echo to trim whitespace:
db='myinivar '
echo -"$(echo $db)"-
-myinivar-
Use crudini which handles these ini file edge cases transparently
db=$(crudini --get config.ini '' DB_USERNAME)
To get rid of more than one trailing space, use %% which removes the longest matching pattern from the end of the string
echo "=${db%% *}="