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How can I use paste and awk inside Perl?

I have the following code that uses 'paste' and AWK script inside Perl.

use strict;              
use Data::Dumper;        
use Carp;
use File::Basename;      

my @files = glob("result/*-*.txt");
my $tocheck = $ARGV[0] || "M";


foreach my $file ( @files  ) {
    my $base = basename($file,".txt");
    my @res = `paste <\(awk '\$4 == "M" {sum += \$2 }END{print sum}' $file \) <\(awk '\$4 == "M" {sum += \$3 }END{print sum}' $file\)`;
    chomp(@res);         
    print "$base $res[0]\n";     
} 

Why it gives such error:

#sh: -c: line 1: syntax error near unexpected token `('
#sh: -c: line 1: `paste <(awk '$4 == "M" {sum += $2 }END{print sum}' result/9547_1-S_aureus.txt ) <(awk '$4 == "M" {sum += $3 }END{print sum}' 
#result/9547_1-S_aureus.txt)

What's the correct way to do it?

like image 971
neversaint Avatar asked Dec 07 '22 07:12

neversaint


2 Answers

Not entirely sure if this is a correct interpretation of your script, as there appears to be a lot of dead/unused code there, but there is certainly no need to go spawning paste or awk to do this:

#!/usr/bin/perl
use warnings;
use strict;
use File::Basename;

my @files = glob ("result/*-*.txt");

foreach my $file (@files) {
   open (FILE, $file) or die "open $file: $!\n";
   # You seem to be summing the 2nd and 3rd columns if the 4th is "M"
   my ($col1, $col2) = (0, 0);
   while (<FILE>) {
       my @cols = split /\s+/;
       if ($cols[3] eq "M") {
          # Perl uses 0-based arrays, unlike awk
          $col1 += $cols[1];
          $col2 += $cols[2];
       }
   }
   close FILE;
   printf "%s %d\n", basename ($file), $col1;
}
like image 75
Bklyn Avatar answered Dec 23 '22 06:12

Bklyn


To address the error, Perl's backtick explicitly uses /bin/sh to run the command. Your /bin/sh isn't like bash and doesn't understand "<(process substitution)" syntax.

I completely agree that calling awk from Perl is just silly.

like image 37
glenn jackman Avatar answered Dec 23 '22 07:12

glenn jackman