I want to make a function in my bash profile to shorten:
awk 'BEGIN{OFS="\t";FS="\t"}{}'
I'd like to be able to type:
awk2 '{print $0}'
And have it do:
awk 'BEGIN{OFS="\t";FS="\t"}{print $0}'
Unless it detects BEGIN in the input...in which case it would revert to the original awk functioning.
Does anyone have any idea what this function would look like?
This is easy if you use awk's -v instead of a BEGIN block.
awk2() {
awk -F'\t' -v OFS='\t' "$#"
}
The -v is used for variable assignments and does take place before line processing.
An alias would be messy, I recommend you shorten it using a bash function:
function awk2() {
awk -F "\t" -v OFS="\t" "$#"
}
Related
Consider this awk script to print column #2 of every line:
awk '{print $2}' a.txt. $2 is not a shell variable, yet when I attempt to submit this code to qsub, $2 is interpreted as such. I.e.
qsub awk '{print $2}' a.txt
results in qsub executing the command
awk '{print }' a.txt
To be clear, I'm not trying to use a shell variable in an awk script; therefore How do I use shell variables in an awk script? is not applicable.
I tried suggestions in Using awk with qsub and issues with quotations, including \$2 and
qsub -- awk '{print $2}' a.txt.
Neither works.
I can certainly put awk in a script and call qsub that way, i.e., qsub awkscript.sh. However, if there's a way to use qsub+awk from the command line, I'd like to learn how.
does a double-layer quoting work, like
qsub 'awk '\''{ print $2 }'\'' a.txt '
RARE Kpop Manifesto below was 99% correct. With a backslash, the whole expression worked like magic :)
qsub 'awk '\''{ print \$2 }'\'' a.txt '
I found some ways to pass external shell variables to an awk script, but I'm confused about ' and ".
First, I tried with a shell script:
$ v=123test
$ echo $v
123test
$ echo "$v"
123test
Then tried awk:
$ awk 'BEGIN{print "'$v'"}'
$ 123test
$ awk 'BEGIN{print '"$v"'}'
$ 123
Why is the difference?
Lastly I tried this:
$ awk 'BEGIN{print " '$v' "}'
$ 123test
$ awk 'BEGIN{print ' "$v" '}'
awk: cmd. line:1: BEGIN{print
awk: cmd. line:1: ^ unexpected newline or end of string
I'm confused about this.
#Getting shell variables into awk
may be done in several ways. Some are better than others. This should cover most of them. If you have a comment, please leave below. v1.5
Using -v (The best way, most portable)
Use the -v option: (P.S. use a space after -v or it will be less portable. E.g., awk -v var= not awk -vvar=)
variable="line one\nline two"
awk -v var="$variable" 'BEGIN {print var}'
line one
line two
This should be compatible with most awk, and the variable is available in the BEGIN block as well:
If you have multiple variables:
awk -v a="$var1" -v b="$var2" 'BEGIN {print a,b}'
Warning. As Ed Morton writes, escape sequences will be interpreted so \t becomes a real tab and not \t if that is what you search for. Can be solved by using ENVIRON[] or access it via ARGV[]
PS If you have vertical bar or other regexp meta characters as separator like |?( etc, they must be double escaped. Example 3 vertical bars ||| becomes -F'\\|\\|\\|'. You can also use -F"[|][|][|]".
Example on getting data from a program/function inn to awk (here date is used)
awk -v time="$(date +"%F %H:%M" -d '-1 minute')" 'BEGIN {print time}'
Example of testing the contents of a shell variable as a regexp:
awk -v var="$variable" '$0 ~ var{print "found it"}'
Variable after code block
Here we get the variable after the awk code. This will work fine as long as you do not need the variable in the BEGIN block:
variable="line one\nline two"
echo "input data" | awk '{print var}' var="${variable}"
or
awk '{print var}' var="${variable}" file
Adding multiple variables:
awk '{print a,b,$0}' a="$var1" b="$var2" file
In this way we can also set different Field Separator FS for each file.
awk 'some code' FS=',' file1.txt FS=';' file2.ext
Variable after the code block will not work for the BEGIN block:
echo "input data" | awk 'BEGIN {print var}' var="${variable}"
Here-string
Variable can also be added to awk using a here-string from shells that support them (including Bash):
awk '{print $0}' <<< "$variable"
test
This is the same as:
printf '%s' "$variable" | awk '{print $0}'
P.S. this treats the variable as a file input.
ENVIRON input
As TrueY writes, you can use the ENVIRON to print Environment Variables.
Setting a variable before running AWK, you can print it out like this:
X=MyVar
awk 'BEGIN{print ENVIRON["X"],ENVIRON["SHELL"]}'
MyVar /bin/bash
ARGV input
As Steven Penny writes, you can use ARGV to get the data into awk:
v="my data"
awk 'BEGIN {print ARGV[1]}' "$v"
my data
To get the data into the code itself, not just the BEGIN:
v="my data"
echo "test" | awk 'BEGIN{var=ARGV[1];ARGV[1]=""} {print var, $0}' "$v"
my data test
Variable within the code: USE WITH CAUTION
You can use a variable within the awk code, but it's messy and hard to read, and as Charles Duffy points out, this version may also be a victim of code injection. If someone adds bad stuff to the variable, it will be executed as part of the awk code.
This works by extracting the variable within the code, so it becomes a part of it.
If you want to make an awk that changes dynamically with use of variables, you can do it this way, but DO NOT use it for normal variables.
variable="line one\nline two"
awk 'BEGIN {print "'"$variable"'"}'
line one
line two
Here is an example of code injection:
variable='line one\nline two" ; for (i=1;i<=1000;++i) print i"'
awk 'BEGIN {print "'"$variable"'"}'
line one
line two
1
2
3
.
.
1000
You can add lots of commands to awk this way. Even make it crash with non valid commands.
One valid use of this approach, though, is when you want to pass a symbol to awk to be applied to some input, e.g. a simple calculator:
$ calc() { awk -v x="$1" -v z="$3" 'BEGIN{ print x '"$2"' z }'; }
$ calc 2.7 '+' 3.4
6.1
$ calc 2.7 '*' 3.4
9.18
There is no way to do that using an awk variable populated with the value of a shell variable, you NEED the shell variable to expand to become part of the text of the awk script before awk interprets it. (see comment below by Ed M.)
Extra info:
Use of double quote
It's always good to double quote variable "$variable"
If not, multiple lines will be added as a long single line.
Example:
var="Line one
This is line two"
echo $var
Line one This is line two
echo "$var"
Line one
This is line two
Other errors you can get without double quote:
variable="line one\nline two"
awk -v var=$variable 'BEGIN {print var}'
awk: cmd. line:1: one\nline
awk: cmd. line:1: ^ backslash not last character on line
awk: cmd. line:1: one\nline
awk: cmd. line:1: ^ syntax error
And with single quote, it does not expand the value of the variable:
awk -v var='$variable' 'BEGIN {print var}'
$variable
More info about AWK and variables
Read this faq.
It seems that the good-old ENVIRON awk built-in hash is not mentioned at all. An example of its usage:
$ X=Solaris awk 'BEGIN{print ENVIRON["X"], ENVIRON["TERM"]}'
Solaris rxvt
You could pass in the command-line option -v with a variable name (v) and a value (=) of the environment variable ("${v}"):
% awk -vv="${v}" 'BEGIN { print v }'
123test
Or to make it clearer (with far fewer vs):
% environment_variable=123test
% awk -vawk_variable="${environment_variable}" 'BEGIN { print awk_variable }'
123test
You can utilize ARGV:
v=123test
awk 'BEGIN {print ARGV[1]}' "$v"
Note that if you are going to continue into the body, you will need to adjust
ARGC:
awk 'BEGIN {ARGC--} {print ARGV[2], $0}' file "$v"
I just changed #Jotne's answer for "for loop".
for i in `seq 11 20`; do host myserver-$i | awk -v i="$i" '{print "myserver-"i" " $4}'; done
I had to insert date at the beginning of the lines of a log file and it's done like below:
DATE=$(date +"%Y-%m-%d")
awk '{ print "'"$DATE"'", $0; }' /path_to_log_file/log_file.log
It can be redirect to another file to save
Pro Tip
It could come handy to create a function that handles this so you dont have to type everything every time. Using the selected solution we get...
awk_switch_columns() {
cat < /dev/stdin | awk -v a="$1" -v b="$2" " { t = \$a; \$a = \$b; \$b = t; print; } "
}
And use it as...
echo 'a b c d' | awk_switch_columns 2 4
Output:
a d c b
How to print the file name in the loop? I want to print the file name and the average value of column 4 at same line:
for i in `ls *cov`
do
awk '{sum +=$4;n++}END{print sum/n}' $i
done
I mean I want to
awk '{sum +=$4;n++}END{print $i\t sum/n}' $i
You can use bash variables in an awk script using the -v flag:
awk -v file=$i '{sum +=$4;n++}END{print file\t sum/n}' $i
But, there is also the built in awk variable FILENAME:
awk '{sum +=$4;n++}END{print FILENAME\t sum/n}' $i
Which is much cleaner since you aren't passing around variables.
Lose the loop (see why-is-using-a-shell-loop-to-process-text-considered-bad-practice) and just use:
awk -v OFS='\t' '{sum+=$4} ENDFILE{print FILENAME, (FNR>0 ? sum/FNR : 0); sum=0}' *cov
The above uses GNU awk for ENDFILE, there's simple tweaks for other awks but the important things are:
A surrounding shell loop is neither required nor desirable.
The variable n isn't needed since awk has builtin variables.
You have to protect yourself from divide by zero on empty files.
I have a text coming in as
A1:B2.C3.D4.E5
A2:B7.C10.D0.E9
A0:B1.C9.D4.E8
I wonder how to change it as
A1:B2.C1.D4.E5
A2:B7.C8.D0.E9
A0:B1.C7.D4.E8
using Awk. First problem is multiple delimiter. Second is, how to get the C-Value and Decrement by 2.
awk solution:
$ awk -F"." '{$2=substr($2,0,1)""substr($2,2)-2;}1' OFS="." file
A1:B2.C1.D4.E5
A2:B7.C8.D0.E9
A0:B1.C7.D4.E8
I was wondering wether awk regexp would do the job, but apparently, awk cannot capture pattern. This is why I suggest perl solution:
$ cat data.txt
A1:B2.C3.D4.E5
A2:B7.C10.D0.E9
A0:B1.C9.D4.E8
$ perl -pe 's/C([0-9]+)/"C" . ($1-2)/ge;' data.txt
A1:B2.C1.D4.E5
A2:B7.C8.D0.E9
A0:B1.C7.D4.E8
Admittedly, I probably would have done this using the substr() function like Guru has shown:
awk 'BEGIN { FS=OFS="." } { $2 = substr($2,0,1) substr($2,2) - 2 }1' file
I do also like Aif's answer using Perl probably just a little more. Shorter is sweeter, isn't it? However, GNU awk can capture pattens. Here's how:
awk 'BEGIN { FS=OFS="." } match($2, /(C)(.*)/, a) { $2 = a[1] a[2] - 2}1' file
I try searching a file by using awk. How can I ask awk to read a variable from the command line as a name to get searched in the file:
this is a regular way I use to search the file and I can ask the user to enter a name to search in the file.txt
awk -f myAwk.awk file.txt
How can I manage it like this :
awk -f myAwk.awk file.txt nameToSearch
How can I use ARGC and ARGV to search the nameToSearch in the file.txt?
What you're probably looking for is
awk [-W option] [-F value] [-v var=value] [--] 'program text' [file ...]
so
awk -v MYVAR=nameToSearch -v OTHERVAR=somethingElse -f myAwk.awk file.txt
Is that it? of course order of switches ( -f, -v ) does not matter. Obvously you then need to include MYVAR ( OTHERVAR ) for a variable identifier inside awk program itself.
To pass a variable to awk, you can use the -v command.
For example:
cat file.txt | awk -v p="stringToSearch" '$0 ~ p'
In this command, tou replace stringToSearch with a pattern (please keep the double quote, they are useful for preserving spaces). The awk command $0 ~ p compares the current line to the given pattern.
Another approach is to build the awk command from the shell:
p="stringToSearch"
awk "/$p/" file.txt
You must use double quotes in the command to force expanding $p.
If it's permitted to change the order of arguments, so that we can do this:
awk -f myAwk.awk nameToSearch file.txt
then you can do:
awk 'NR==1 { nameToSearch = $0; next} { ... rest of myAwk.awk here ...}' nameToSearch file.txt
You can of course add the NR==1 {...} block to the beginning of your myAwk.awk file, then continue using:
awk -f myAwk.awk nameToSearch file.txt
The technique Piotr Wadas describes has the same effect:
awk -v nameToSearch=whatever -f myAwk.awk file.txt
and that's what I'd use myself, rather than passing whatever as an additional argument to the script. Passing whatever as an additional argument is what scripters had to do before the -v facilities were added to awk. If writing -v nameToSearch= is too verbose, then I'd wrap the whole thing up in a shell script, and say:
myShellScript whatever file.txt
But you asked how to do it by passing whatever as an additional argument to the awk script, so that's what I demonstrated.