this is probably a very stupid question; in a bash script, given the output of, for instance;
awk '{print $7}' temp
it gives 0.54546
I would like to give this to a variable, so I tried:
read ENE <<< $(awk '{print $7}' temp)
but I get
Syntax error: redirection unexpected
Could you tell me why, and what is the easiest way to do this assignment?
Thanks
You can do command substitution as:
ENE=$(awk '{print $7}' temp)
or
ENE=`awk '{print $7}' temp`
This will assign the value 0.54546 to the variable ENE
your syntax should be
read ENE <<<$(awk '{print $1}' file)
you can directly assign the value as well
ENE=$(awk '{print $7}' temp)
you can also use the shell
$ var=$(< temp)
$ set -- $var
$ echo $7
or you can read it into array
$ declare -a array
$ read -a array <<<$(<file)
$ echo ${array[6]}
In general, Bash is kinda sensitive to spaces (requiring them some places, and breaking if they are added to other places,) which in my opinion is too bad. Just remember that there should be no space on either side of an equal sign, there should be no space after a dollar sign, and parentheses should be lined with spaces ( like this ) (not like this.)
`command` and $( command ) are the same thing, but $( this version can be $( nested ) ) whereas "this version can be `embedded in strings.` "
Related
I have a file that looks like:
>ref_frame=1
TPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPFRKQNPDIVIYQYMDDLYVGSD
>ref_frame=2
HQGLDISTMCFHRDGKDHQQYSKVA*QKS*SLLENKIQT*LSINTWMICM*DLT
>ref_frame=3
TRD*ISVQCASTGMERITSNIPK*HDKNLRAF*KTKSRHSYLSIHG*FVCRI*
>test_3_2960_3_frame=1
TPGIRYQYNVLPQGWKGSPAIFQSSMTKILEPSRKQNPDIVIYQYMDDLYVGSD
I want to assign a bash variable so that echo $variable gives test_3_2960
The line/row that I want to assign the variable to will always be line 7. How can I accomplish this using bash?
so far I have:
variable=`cat file.txt | awk 'NR==7'`
echo $variable = >test_3_2960_3_frame=1
Using sed
$ variable=$(sed -En '7s/>(([^_]*_){2}[0-9]+).*/\1/p' input_file)
$ echo "$variable"
test_3_2960
No pipes needed here...
$: variable=$(awk -F'[>_]' 'NR==7{ OFS="_"; print $2, $3, $4; exit; }' file)
$: echo $variable
test_3_2960
-F is using either > or _ as field separators, so your data starts in field 2.
OFS="_" sets the Output Field Separator, but you could also just use "_" instead of commas.
exit keeps it from wasting time bothering to read beyond line 7.
If you wish to continue with awk
$ variable=$(awk 'NR==7' file.txt | awk -F "[>_]" '{print $2"_"$3"_"$4}')
$ echo $variable
test_3_2960
I have a simple command (part of a bash script) that I'm piping through awk but can't seem to suppress the final record separator without then piping to sed. (Yes, I have many choices and mine is sed.) Is there a simpler way without needing the last pipe?
dolls = $(egrep -o 'alpha|echo|november|sierra|victor|whiskey' /etc/passwd \
| uniq | awk '{IRS="\n"; ORS=","; print}'| sed s/,$//);
Without the sed, this produces output like echo,sierra,victor, and I'm just trying to drop the last comma.
You don't need awk, try:
egrep -o ....uniq|paste -d, -s
Here is another example:
kent$ echo "a
b
c"|paste -d, -s
a,b,c
Also I think your chained command could be simplified. awk could do all things in an one-liner.
Instead of egrep, uniq, awk, sed etc, all this can be done in one single awk command:
awk -F":" '!($1 in a){l=l $1 ","; a[$1]} END{sub(/,$/, "", l); print l}' /etc/password
Here is a small and quite straightforward one-liner in awk that suppresses the final record separator:
echo -e "alpha\necho\nnovember" | awk 'y {print s} {s=$0;y=1} END {ORS=""; print s}' ORS=","
Gives:
alpha,echo,november
So, your example becomes:
dolls = $(egrep -o 'alpha|echo|november|sierra|victor|whiskey' /etc/passwd | uniq | awk 'y {print s} {s=$0;y=1} END {ORS=""; print s}' ORS=",");
The benefit of using awk over paste or tr is that this also works with a multi-character ORS.
Since you tagged it bash here is one way of doing it:
#!/bin/bash
# Read the /etc/passwd file in to an array called names
while IFS=':' read -r name _; do
names+=("$name");
done < /etc/passwd
# Assign the content of the array to a variable
dolls=$( IFS=, ; echo "${names[*]}")
# Display the value of the variable
echo "$dolls"
echo "a
b
c" |
mawk 'NF-= _==$NF' FS='\n' OFS=, RS=
a,b,c
Is there a way to set a variable in my current shell from within awk?
I'd like to do some processing on a file and print out some data; since I'll read the whole file through, I'd like to save the number of lines -- in this case, FNR.
Happens though I can't seem to find a way to set a shell variable with FNR value; if not this, I'd have to read the FNR from my output file, to set, say num_lines, with FNR value.
I've tried some combinations using awk 'END{system(...)}', but could not manage it to work. Any way around this?
Here's another way.
This is especially useful when when you've got the values of your variables in a single variable and you want split them up. For example, you have a list of values from a single row in a database that you want to create variables out of.
val="hello|beautiful|world" # assume this string comes from a database query
read a b c <<< $( echo ${val} | awk -F"|" '{print $1" "$2" "$3}' )
echo $a #hello
echo $b #beautiful
echo $c #world
We need the 'here string' i.e <<< in this case, because the read command does not read from a pipe and instead reads from stdin
$ echo "$var"
$ declare $( awk 'BEGIN{print "var=17"}' )
$ echo "$var"
17
Here's why you should use declare instead of eval:
$ eval $( awk 'BEGIN{print "echo \"removing all of your files, ha ha ha....\""}' )
removing all of your files, ha ha ha....
$ declare $( awk 'BEGIN{print "echo \"removing all of your files\""}' )
bash: declare: `"removing': not a valid identifier
bash: declare: `files"': not a valid identifier
Note in the first case that eval executes whatever string awk prints, which could accidentally be a very bad thing!
You can't export variables from a subshell to its parent shell. You have some other choices, though, including:
Make another pass of the file using AWK to count records, and use command substitution to capture the result. For example:
FNR=$(awk 'END {print FNR}' filename)
Print FNR in the subshell, and parse the output in your other process.
If FNR is the same as number of lines, you can call wc -l < filename to get your count.
A warning for anyone trying to use declare as suggested by several answers.
eval does not have this problem.
If the awk (or other expression) provided to declare results in an empty string then declare will dump the current environment.
This is almost certainly not what you would want.
eg: if your awk pattern doesn't exist in the input you will never print an output, therefore you will end up with unexpected behaviour.
An example of this....
unset var
var=99
declare $( echo "foobar" | awk '/fail/ {print "var=17"}' )
echo "var=$var"
var=99
The current environment as seen by declare is printed
and $var is not changed
A minor change to store the value to set in an awk variable and print it at the end solves this....
unset var
var=99
declare $( echo "foobar" | awk '/fail/ {tmp="17"} END {print "var="tmp}' )
echo "var=$var"
var=
This time $var is unset ie: set to the null string var=''
and there is no unwanted output.
To show this working with a matching pattern
unset var
var=99
declare $( echo "foobar" | awk '/foo/ {tmp="17"} END {print "var="tmp}' )
echo "var=$var"
var=
This time $var is unset ie: set to the null string var=''
and there is no unwanted output.
Make awk print out the assignment statement:
MYVAR=NewValue
Then in your shell script, eval the output of your awk script:
eval $(awk ....)
# then use $MYVAR
EDIT: people recommend using declare instead of eval, to be slightly less error-prone if something other than the assignment is printed by the inner script. It's bash-only, but it's okay when the shell is bash and the script has #!/bin/bash, correctly stating this dependency.
The eval $(...) variant is widely used, with existing programs generating output suitable for eval but not for declare (lesspipe is an example); that's why it's important to understand it, and the bash-only variant is "too localized".
To synthesize everything here so far I'll share what I find is useful to set a shell environment variable from a script that reads a one-line file using awk. Obviously a /pattern/ could be used instead of NR==1 to find the needed variable.
# export a variable from a script (such as in a .dotfile)
declare $( awk 'NR==1 {tmp=$1} END {print "SHELL_VAR=" tmp}' /path/to/file )
export SHELL_VAR
This will avoid a massive output of variables if a declare command is issued with no argument, as well as the security risks of a blind eval.
echo "First arg: $1"
for ((i=0 ; i < $1 ; i++)); do
echo "inside"
echo "Welcome $i times."
cat man.xml | awk '{ x[NR] = $0 } END { for ( i=2 ; i<=NR ; i++ ) { if (x[i] ~ // ) {x[i+1]=" '$i'"}print x[i] }} ' > $i.xml
done
echo "compleated"
Trying to pass a variable into awk from user input:
Have tried variations of awk -v with errors stating 'awk: invalid -v option', even though the option is listed in man files.
#! /bin/bash
read -p "Enter ClassID:" CLASS
read -p "Enter FacultyName:" FACULTY
awk '/FacultyName/ {print}' data-new.csv > $FACULTY.csv
awk -vclass=${CLASS} '/class/ {print}' data-new.csv >> $FACULTY.csv
echo Class is $CLASS
echo Faculty member is $FACULTY
Some versions of awk require a space between the -v and the variable assignment. Also, you should put the bash variable in double-quotes to prevent unwanted parsing by the shell (e.g. word splitting, wildcard expansion) before it's passed to awk. Finally, in awk /.../ is a constant regular expression (i.e. /class/ will search for the string "class", not the value of the variable "class"). With all of this corrected, here's the awk command that I think will do what you want:
awk -v class="${CLASS}" '$0 ~ class {print}' data-new.csv >> $FACULTY.csv
Now, is there any reason you're using this instead of:
grep "$CLASS" data-new.csv >> $FACULTY.csv
Your script is not clear to me, but these all work:
CLASS=ec123
echo | awk -vclass=$CLASS '{print class}'
echo | awk -vclass=${CLASS} '{print class}'
I would like to use the lines coming from 'wc' as variables. For example:
echo 'foo bar' > file.txt
echo 'blah blah blah' >> file.txt
wc file.txt
2 5 23 file.txt
I would like to have something like $lines, $words and $characters associated to the values 2, 5, and 23. How can I do that in bash?
In pure bash: (no awk)
a=($(wc file.txt))
lines=${a[0]}
words=${a[1]}
chars=${a[2]}
This works by using bash's arrays. a=(1 2 3) creates an array with elements 1, 2 and 3. We can then access separate elements with the ${a[indice]} syntax.
Alternative: (based on gonvaled solution)
read lines words chars <<< $(wc x)
Or in sh:
a=$(wc file.txt)
lines=$(echo $a|cut -d' ' -f1)
words=$(echo $a|cut -d' ' -f2)
chars=$(echo $a|cut -d' ' -f3)
There are other solutions but a simple one which I usually use is to put the output of wc in a temporary file, and then read from there:
wc file.txt > xxx
read lines words characters filename < xxx
echo "lines=$lines words=$words characters=$characters filename=$filename"
lines=2 words=5 characters=23 filename=file.txt
The advantage of this method is that you do not need to create several awk processes, one for each variable. The disadvantage is that you need a temporary file, which you should delete afterwards.
Be careful: this does not work:
wc file.txt | read lines words characters filename
The problem is that piping to read creates another process, and the variables are updated there, so they are not accessible in the calling shell.
Edit: adding solution by arnaud576875:
read lines words chars filename <<< $(wc x)
Works without writing to a file (and do not have pipe problem). It is bash specific.
From the bash manual:
Here Strings
A variant of here documents, the format is:
<<<word
The word is expanded and supplied to the command on its standard input.
The key is the "word is expanded" bit.
lines=`wc file.txt | awk '{print $1}'`
words=`wc file.txt | awk '{print $2}'`
...
you can also store the wc result somewhere first.. and then parse it.. if you're picky about performance :)
Just to add another variant --
set -- `wc file.txt`
chars=$1
words=$2
lines=$3
This obviously clobbers $* and related variables. Unlike some of the other solutions here, it is portable to other Bourne shells.
I wanted to store the number of csv file in a variable. The following worked for me:
CSV_COUNT=$(ls ./pathToSubdirectory | grep ".csv" | wc -l | xargs)
xargs removes the whitespace from the wc command
I ran this bash script not in the same folder as the csv files. Thus, the pathToSubdirectory
You can assign output to a variable by opening a sub shell:
$ x=$(wc some-file)
$ echo $x
1 6 60 some-file
Now, in order to get the separate variables, the simplest option is to use awk:
$ x=$(wc some-file | awk '{print $1}')
$ echo $x
1
declare -a result
result=( $(wc < file.txt) )
lines=${result[0]}
words=${result[1]}
characters=${result[2]}
echo "Lines: $lines, Words: $words, Characters: $characters"