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 % ':'.
Related
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 have a string like this:
/var/cpanel/users/joebloggs:DNS9=domain.example
I need to extract the username (joebloggs) from this string and store it in a variable.
The format of the string will always be the same with exception of joebloggs and domain.example so I am thinking the string can be split twice using cut?
The first split would split by : and we would store the first part in a variable to pass to the second split function.
The second split would split by / and store the last word (joebloggs) into a variable
I know how to do this in PHP using arrays and splits but I am a bit lost in bash.
To extract joebloggs from this string in bash using parameter expansion without any extra processes...
MYVAR="/var/cpanel/users/joebloggs:DNS9=domain.example"
NAME=${MYVAR%:*} # retain the part before the colon
NAME=${NAME##*/} # retain the part after the last slash
echo $NAME
Doesn't depend on joebloggs being at a particular depth in the path.
Summary
An overview of a few parameter expansion modes, for reference...
${MYVAR#pattern} # delete shortest match of pattern from the beginning
${MYVAR##pattern} # delete longest match of pattern from the beginning
${MYVAR%pattern} # delete shortest match of pattern from the end
${MYVAR%%pattern} # delete longest match of pattern from the end
So # means match from the beginning (think of a comment line) and % means from the end. One instance means shortest and two instances means longest.
You can get substrings based on position using numbers:
${MYVAR:3} # Remove the first three chars (leaving 4..end)
${MYVAR::3} # Return the first three characters
${MYVAR:3:5} # The next five characters after removing the first 3 (chars 4-9)
You can also replace particular strings or patterns using:
${MYVAR/search/replace}
The pattern is in the same format as file-name matching, so * (any characters) is common, often followed by a particular symbol like / or .
Examples:
Given a variable like
MYVAR="users/joebloggs/domain.example"
Remove the path leaving file name (all characters up to a slash):
echo ${MYVAR##*/}
domain.example
Remove the file name, leaving the path (delete shortest match after last /):
echo ${MYVAR%/*}
users/joebloggs
Get just the file extension (remove all before last period):
echo ${MYVAR##*.}
example
NOTE: To do two operations, you can't combine them, but have to assign to an intermediate variable. So to get the file name without path or extension:
NAME=${MYVAR##*/} # remove part before last slash
echo ${NAME%.*} # from the new var remove the part after the last period
domain
Define a function like this:
getUserName() {
echo $1 | cut -d : -f 1 | xargs basename
}
And pass the string as a parameter:
userName=$(getUserName "/var/cpanel/users/joebloggs:DNS9=domain.example")
echo $userName
What about sed? That will work in a single command:
sed 's#.*/\([^:]*\).*#\1#' <<<$string
The # are being used for regex dividers instead of / since the string has / in it.
.*/ grabs the string up to the last backslash.
\( .. \) marks a capture group. This is \([^:]*\).
The [^:] says any character _except a colon, and the * means zero or more.
.* means the rest of the line.
\1 means substitute what was found in the first (and only) capture group. This is the name.
Here's the breakdown matching the string with the regular expression:
/var/cpanel/users/ joebloggs :DNS9=domain.example joebloggs
sed 's#.*/ \([^:]*\) .* #\1 #'
Using a single Awk:
... | awk -F '[/:]' '{print $5}'
That is, using as field separator either / or :, the username is always in field 5.
To store it in a variable:
username=$(... | awk -F '[/:]' '{print $5}')
A more flexible implementation with sed that doesn't require username to be field 5:
... | sed -e s/:.*// -e s?.*/??
That is, delete everything from : and beyond, and then delete everything up until the last /. sed is probably faster too than awk, so this alternative is definitely better.
Using a single sed
echo "/var/cpanel/users/joebloggs:DNS9=domain.example" | sed 's/.*\/\(.*\):.*/\1/'
I like to chain together awk using different delimitators set with the -F argument. First, split the string on /users/ and then on :
txt="/var/cpanel/users/joebloggs:DNS9=domain.com"
echo $txt | awk -F"/users/" '{print$2}' | awk -F: '{print $1}'
$2 gives the text after the delim, $1 the text before it.
I know I'm a little late to the party and there's already good answers, but here's my method of doing something like this.
DIR="/var/cpanel/users/joebloggs:DNS9=domain.example"
echo ${DIR} | rev | cut -d'/' -f 1 | rev | cut -d':' -f1
To get what is between "aa=" and either % or empty
string = "aa=value%bb"
string2 = "bb=%aa=value"
The rule must work on both strings to get the value of "aa="
I would like a BASH LANGUAGE solution if possible.
Use this:
result=$(echo "$string" | grep -o 'aa=[^%]*')
result=${result:3} # remove aa=
[^%]* matches any sequence of characters that doesn't contain %, so it will stop when it gets to % or the end of the string. $(result:3} expands to the substring starting from character 3, which removes aa= from the beginning.
I'm reading in values from an .ini file, and sometimes may get trailing or leading whitespace.
How do I amend this first line to prevent that?
db=$(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%% *}="
I have a string which i need to insert at a specific position in a file :
The file contains multiple semicolons(;) i need to insert the string just before the last ";"
Is this possible with SED ?
Please do post the explanation with the command as I am new to shell scripting
before :
adad;sfs;sdfsf;fsdfs
string = jjjjj
after
adad;sfs;sdfsf jjjjj;fsdfs
Thanks in advance
This might work for you:
echo 'adad;sfs;sdfsf;fsdfs'| sed 's/\(.*\);/\1 jjjjj;/'
adad;sfs;sdfsf jjjjj;fsdfs
The \(.*\) is greedy and swallows the whole line, the ; makes the regexp backtrack to the last ;. The \(.*\) make s a back reference \1. Put all together in the RHS of the s command means insert jjjjj before the last ;.
sed 's/\([^;]*\)\(;[^;]*;$\)/\1jjjjj\2/' filename
(substitute jjjjj with what you need to insert).
Example:
$ echo 'adad;sfs;sdfsf;fsdfs;' | sed 's/\([^;]*\)\(;[^;]*;$\)/\1jjjjj\2/'
adad;sfs;sdfsfjjjjj;fsdfs;
Explanation:
sed finds the following pattern: \([^;]*\)\(;[^;]*;$\). Escaped round brackets (\(, \)) form numbered groups so we can refer to them later as \1 and \2.
[^;]* is "everything but ;, repeated any number of times.
$ means end of the line.
Then it changes it to \1jjjjj\2.
\1 and \2 are groups matched in first and second round brackets.
For now, the shorter solution using sed : =)
sed -r 's#;([^;]+);$#; jjjjj;\1#' <<< 'adad;sfs;sdfsf;fsdfs;'
-r option stands for extented Regexp
# is the delimiter, the known / separator can be substituted to any other character
we match what's finishing by anything that's not a ; with the ; final one, $ mean end of the line
the last part from my explanation is captured with ()
finally, we substitute the matching part by adding "; jjjj" ans concatenate it with the captured part
Edit: POSIX version (more portable) :
echo 'adad;sfs;sdfsf;fsdfs;' | sed 's#;\([^;]\+\);$#; jjjjj;\1#'
echo 'adad;sfs;sdfsf;fsdfs;' | sed -r 's/(.*);(.*);/\1 jjjj;\2;/'
You don't need the negation of ; because sed is by default greedy, and will pick as much characters as it can.
sed -e 's/\(;[^;]*\)$/ jjjj\1/'
Inserts jjjj before the part where a semicolon is followed by any number of non-semicolons ([^;]*) at the end of the line $. \1 is called a backreference and contains the characters matched between \( and \).
UPDATE: Since the sample input has no longer a ";" at the end.
Something like this may work for you:
echo "adad;sfs;sdfsf;fsdfs"| awk 'BEGIN{FS=OFS=";"} {$(NF-1)=$(NF-1) " jjjjj"; print}'
OUTPUT:
adad;sfs;sdfsf jjjjj;fsdfs
Explanation: awk starts with setting FS (field separator) and OFS (output field separator) as semi colon ;. NF in awk stands for number of fields. $(NF-1) thus means last-1 field. In this awk command {$(NF-1)=$(NF-1) " jjjjj" I am just appending jjjjj to last-1 field.