CODEWITHSUNDEEP
linuxbashshellvariablesawk
njBernstein
njBernstein

Reputation: 115

How to pass string or variable as multiple parameters for awk within a bash scripts?

I'm trying to pass a variable, $formula into an awk script:

[node2 filtering]$ echo $formula
$25 ~ "1/1" && $24 ~ "1/1" && $23 ~ "1/1" && $22 ~ "1/1" && $21 ~ "1/1" && $20 ~ "1/1" && $19 ~ "1/1" && $18 ~ "1/1" && $17 ~ "1/1" && $16 ~ "1/1" && $15 ~ "1/1" && $14 ~ "1/1" && $13 ~ "1/1" && $12 ~ "1/1" && $11 ~ "1/1" && $10 ~ "1/1"||$10 ~ "0/1" && $11 ~ "0/1" && $12 ~ "0/1" && $13 ~ "0/1" && $14 ~ "0/1" && $15 ~ "0/1" && $16 ~ "0/1" && $17 ~ "0/1" && $18 ~ "0/1" && $19 ~ "0/1" && $20 ~ "0/1" && $21 ~ "0/1" && $22 ~ "0/1" && $23 ~ "0/1" && $24 ~ "0/1" && $25 ~ "0/1"

I'm trying to pass into the following to filter my text file, but when I do no filtering happens. I don't get an error either.

awk -F\\t  -v myvar="$formula" 'myvar {print $0}' myfile

This works:

awk -F\\t '$10 ~ "0/1" + $11 ~ "0/1"+ $12 ~ "0/1"+ $13 ~ "0/1"+ $14 ~ "0/1"{print $0}' myflies

The reason I'm trying to do this is that I have a simple for loop, which creates $formula based on the number of columns I want to filter. The number of columns I decide to filter upon is simply based on the number of subjects in the experiment and will always be $10 to $(10+n) where n is the number of subjects.

Any ideas or tips would be greatly appreciated as to how to solve this problem or construct my script in a different manner?

Here's the silly for loop to construct $formula:

blah1=$(echo "")
blah2=$(echo "")
for (( i=1; i <= $NUMBEROFSUBJECTS; i++ ))
    do
     l=$(echo $(( i + $minus )))``

    if [ $i == 1 ] ; then
             blah1=$(echo " \$$l ~ \"1/1\" ")
             blah2=$(echo " \$$l ~ \"0/1\" ")
    else
            inter1=$(echo " \$$l ~ \"1/1\" ")
            blah1=$(echo $inter1 + $blah1)

            inter2=$(echo " \$$l ~ \"0/1\" ")
            blah2=$(echo $blah2+$inter2)
    fi
done
formula=$(echo $blah1  " || " $blah2)`

Here's where I got the awk -F\\t -v myvar="$formula" 'myvar {print $0}' idea from:

Howto Pass A String as Parameter in AWK within Bash Script

edit: Answer that worked for me ended up being: 

 awk -F\\t "$formula"'{print $0}' myfile

Thanks so much everyone. Sorry it ended up being so simple.

Upvotes: 1

Views: 509

Answers (1)

yacc
yacc

Reputation: 3361

Do something like this:

formula="$blah1|$blah2"
...
awk "/$formula/ {...}"

So the proposal is to skip the variable definition and just rely on the shell substitution.

Upvotes: 2

Related Questions