Error in substitution in perl

Question

#!/usr/bin/perl                                                                                                                                                                  

use strict;
use warnings;

my $directory = shift @ARGV or die "Please specify a directory";

if(opendir(DIR , $directory))

{
    my @files = readdir(DIR);

    @files = grep(/\.out/ , @files);

    closedir(DIR);

    foreach my $file (@files)
    {
        if ( -z $directory.$file )
        {
            next;
        }
        ProcessData($directory.$file);
    }

}
else
{
    print STDERR "unable to open current directory\n";
}

sub ProcessData
{
    my ($file) = @_;

    if(open(FILE , $file))
    {
        my @lines = <FILE>;
        my $lines =~ s/\,//g;
        my @fields = split(/\s+/,$lines[1]);

        print "$fields[1] $fields[2] $fields[3] $fields[4] $fields[5]\n";

        close FILE;
    }

    else
    {
        print STDERR "Can't open $file\n";
    }

I'm trying to split the second line of a set of files on white space, remove all commas, and then print some of the fields. The correct fields are printed but the comma remains, and I am given the error message: Use of uninitialized value $lines in substitution (s///). I am fairly new to Perl and quite confused by this. Any help would be hugely appreciated. Thanks in advance.

Can you show some example input and what you expect the output to be? There are probably a couple things you'll want to change. — hmatt1, Feb 22 '14 at 18:11
Sorry - this is from a subroutine, use strict is at the beginning of the code. The input is this Header: UniProtAC, Nat, Resnum, Mut, Prediction, Confidence AvrgALL: P06132, ARG, 332, HIS, PD, 0.62 — user3341369, Feb 22 '14 at 18:17
with AvrgALL being the start of the second line. Ideally the output would be P06132 ARG 332 HIS PD but currently each of these are followed by a comma when I run the script — user3341369, Feb 22 '14 at 18:18

score 0 · Accepted Answer · edited May 23 '17 at 10:31

0

Ok you weren't too far off. The problem is that you wrote my $lines =~ s/\,//g; instead of $lines[1] =~ s/\,//g;.

#!/bin/perl
use strict;
use warnings;

my $file = "input.txt";
open my $fh, "<", $file or die "$!";

my @lines = <$fh>;
$lines[1] =~ s/\,//g; # This is the line that needed to be fixed
my @fields = split('\s+', $lines[1]);
print "$fields[1] $fields[2] $fields[3] $fields[4] $fields[5]\n";
close $fh;

Output:

$ cat input.txt
UniProtAC, Nat, Resnum, Mut, Prediction, Confidence
AvrgALL: P06132, ARG, 332, HIS, PD, 0.62
$ perl sub.pl
P06132 ARG 332 HIS PD

Another thing I want to point out is answered here: What's the best way to open and read a file in Perl?. Using the 3 argument form of open is generally better, and so is using lexical file handles.

edited May 23 '17 at 10:31

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answered Feb 22 '14 at 18:26

hmatt1

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Thanks a lot for your help. I perhaps should have posted the whole script to make things clearer or in case someone else finds it useful: – user3341369 Feb 22 '14 at 18:33
will do - does the full code (just added) make it clearer what i was trying to do? – user3341369 Feb 22 '14 at 18:37
Yeah it's clear! You're trying to print the 5 fields for each file that ends with `.out` in the specified folder. I just tested it and it works as expected (with that 1 line changed). Remember to call it like `perl script.pl folder/`, you'll need the slash at the end of your folder name. – hmatt1 Feb 22 '14 at 18:45
If i change $lines to $lines[1] I now get: "my" variable @lines masks earlier declaration in same scope at ./processPredictorData3.pl line 38. syntax error at ./processPredictorData3.pl line 38, near "$lines[" Execution of ./processPredictorData3.pl aborted due to compilation errors. Thanks again for your help! Any ideas what the issue is? – user3341369 Feb 22 '14 at 18:45
Don't include the `my`, just `$lines[1] =~ s/\,//g;` – hmatt1 Feb 22 '14 at 18:47

Error in substitution in perl

1 Answers1