cburger has asked for the wisdom of the Perl Monks concerning the following question:

Hi, I'm trying to change directories within a perl script, but for some reason it doesn't follow correctly into the right directory. Here is the code, if you know what's wrong with it - help is a lot appreciated! Thanks. 

 

#!/usr/bin/perl

use File::chdir;
use Cwd;
use strict;
my $dir='/data1/sgb';

chdir '$dir/Hsapiens_fasta_folder';

my @files=<*.fa>;

chdir '$dir/targetp-1.1';

my $current=getcwd();

foreach my $file( @files) {
print "$file\n";
print "$current\n";

}

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so what happens in this script is that instead of print at $current : chdir '$dir/targetp-1.1'; it prints '/data1/sgb'; - i.e. the location of $dir. I have no idea why. Thanks for the help.

Replies are listed 'Best First'.
Re: using change directory within perl script
by tangent (Parson) on Mar 27, 2012 at 04:22 UTC
    The variable $dir is not interpolated when you use single quotes, try changing them to doubles: "$dir/Hsapiens_fasta_folder"

    The idea of File::chdir is to not use chdir() and use $CWD instead: 
    #!/usr/bin/perl
use strict;
use File::chdir;
my $dir = '/data1/sgb';
$CWD = "$dir/Hsapiens_fasta_folder";
my @files=<*.fa>;
$CWD = "$dir/targetp-1.1";
foreach my $file( @files) {
    print "$file\n";
    print "$CWD\n";
}

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      ThANKS A LOT ...VERY HELPFUL
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Re: using change directory within perl script
by jwkrahn (Abbot) on Mar 27, 2012 at 04:16 UTC 
    use File::chdir;

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    Did you read the documentation for this module?    You are not using it anywhere in this program. 



    chdir '$dir/Hsapiens_fasta_folder';
...
chdir '$dir/targetp-1.1';

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    You should verify that these functions worked correctly: 

    chdir '$dir/Hsapiens_fasta_folder' or warn "Cannot chdir to '$dir/Hsap
+iens_fasta_folder' because: $!";
...
chdir '$dir/targetp-1.1' or warn "Cannot chdir to '$dir/targetp-1.1' b
+ecause: $!";

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Re: using change directory within perl script
by bms (Monk) on Mar 27, 2012 at 04:11 UTC

    Why are you using chdir with File::chdir?

    Try using it like:

    ...
use File::chdir;

$CWD = '/usr/bin'; # Oh hey, in /usr/bin/
...

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    Or

    ...
use File::chdir;

$CWD = '/home/me/perl'; # Now in /home/me/perl

{
    local $CWD = '/home/you/python'; # Now in /home/you/python
    ...
}

# Back in /home/me/perl
...

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    Hope this helps!

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      What if chdir.pm is not avaialble at /usr/lib/perl5/5.8.8/File ? Is there any other alternate way to change directory?
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