Question

I want to make an array in Perl with the values obtained from my awk script. Then I can do math on them in Perl.

Here is my Perl, which runs a program, which saves a text file:

my $unix_command_dsc = (`./program -s test.fasta saved_file.txt`);
my $dsc_run = qx($unix_command_dsc);

Now I have some Awk that parses that data saved in the text file:

#!/usr/bin/awk -f

BEGIN{       # Initialize the values to zero. Note, done automatically also.
    sumc4 = 0
    sumc5 = 0
    sumc6 = 0
}

/^[1-9][0-9]* residue/ {next}    #Match line that begins with number and has word 'residue', skip it.
/^[1-9]/ {                       #Match line that begins with number.

    sumc4 += $4                  #Add up the values of the nth column into the variables.
    sumc5 += $5
    sumc6 += $6

    print $4 "\t" $5 "\t" $6    #This will show the whole columns. 

    }

END{
    print "sum H" "\t" "sum E" "\t" "sum C"
    print sumc4 "\t" sumc5 "\t" sumc6  
}

I run this Awk from terminal with the following commands:

./awk_program.txt saved_file.txt 

Any ideas how I would gather this data from the print statements in awk into arrays in perl?

What I’ve tried is to just run that awk script in perl:

my $unix_command_awk = (`./awk_program.txt saved_file.txt`);
my $awk_run = qx($unix_command_awk);

But perl gives me errors and commands not found, like it thinks the data are commands. Should there be a STDOUT in the awk that I’m missing, rather than print?

Answer 1

It should just be:

my $awk_run = `./awk_program.txt saved_file.txt`;

Backticks tell perl to run the command and return the output. So your assignment to $unix_command_awk is running the command, and then qx($unix_command_awk) executes the output as a new command.