Is it related to creating a directory using the string in $output, but trying to open a directory using the string in $dirname?

BTW, don't comment out strictures - ever!

Do use the three parameter version of open and use lexical file handles:

open my $inputFile1, '<', $input or die " Cannot open file $input: $!"
+;
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#!/usr/local/bin/perl -w
# use strict;
# use warnings;
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That should be:

#!/usr/local/bin/perl
use strict;
use warnings;
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if($#ARGV != 1)
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That is usually written as:

if(@ARGV != 2)
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chomp(@ARGV);
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There is no need to chomp the @ARGV array!

$dirname =~ s/\/$//g;
$output  =~ s/\/$//g;
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You are anchoring the pattern to the end of the string so the /g option is superfluous.

mkdir $output if (-d $output ==0);
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That would usually be written as:

mkdir $output or die "mkdir $output: $!" unless -d $output;
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Huh? Where has the OP code gone?

Original question (code tags fixed):

I am trying to output the file to a new directory ( the files to be modified is in another folder) but i am getting the error cannot open directory

My code:

#!/usr/local/bin/perl -w
# use strict;
# use warnings;
if($#ARGV != 1)
{
    print "usage: perl directory.pl source direcoty  detination direct
+ory \n";
    exit;
}

chomp(@ARGV);
#my $dirname = "lab";
#my $output="lab2";

my $dirname = $ARGV[0];
my $output= $ARGV[1];

$dirname =~ s/\/$//g;
$output  =~ s/\/$//g;

mkdir $output if (-d $output ==0);
#`rm $output/*.lab`;
opendir(DIR, $dirname) or die "can't opendir $dirname: $!";

while (defined($file = readdir(DIR))) {
$file2=$file;
$input=$dirname."/".$file;
$out=$output."/".$file2;
print $file."\t".$input."\t".$out."\n";


open(F,"<$input") or die " Cannot open file $input: $!";
open(F1,">$out") or die " Cannot open file $out: $!";

<F>;

#while ($line = readline(F)) {

#$line=~s/^(.*)\n$/$1/s;
#$line=~  s/\r//gi; 
#print F1 $line ;
#}
close (F);
close (F1);
}
closedir(DIR);
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