I am trying to change the name of several files from some like "sample_ACCTGG.fq" to some like "LA01.fq" based in a file with the interchangeable names (ID.txt). This files is in a format where the separation between columns are tabs and looks like 

LA01 ACCTGG
LA02 ATTGGC
LA03 ATCCCG

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I wrote this scrip 

 
#!/usr/bin/perl
opendir(DIR, "/samplesA") or die "Can not open folder, $!\n";
@files = readdir(DIR);
closedir (DIR);
open (IN,"</ID.txt")or die "Can not open barcode file, $!\n";
@lines=(<IN>);
close IN;
foreach $file (@files)
{
if ($file =~ m/fq$/)
{
foreach $line (@lines)
{
        my ($id, $barcode) = split(/\t/,$line);
if ($file =~ m/$barcode/)
{
        my $new = $file;
        $new =~ s/sample_$barcode/$id/;
        rename ($file, $new) or die "Can not change $file to $new, $!\
+n";
}}}}

[download]

it works for the first files, buy then die with the massage "Can not change sample_ACCTGG.fq to ACCTGG.fq". But when I print $new, it is "LA01.fq" that is correct.

In reply to change files names bug by Yuma248

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