which?

$!

Yep the lines are chomped in fact if you print $barcodes print the right string without new line

You said 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.

but the code is  rename ($file, $new) or die "Can not change $file to $new, $!\n"; so the error message you quoted is incomplete, it doesn't state the reason it rename didn't work

This reason is everything

readdir does NOT return the complete path, so 'ACCTGG.fg' is not the same file as 'samplesA/ACCTGG.fg' .

my @RegExp = /^([A-Za-z]{2}\d{2,})\s+(.*)$/g;
[download]

Yep I am sure the space between columns is tab, in fact when you print $id or $barcode you get the right strings inclusive if you print them just before the rename command

How about undoing some of those loops. If your file names are as consistent as they look from your example, this is a simpler way to do it

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

# Read barcodes, and look for coresponding files to rename
my $dir = "/samplesA";
my $bcf = "/ID.txt";
open my $barcodelist, "<", $bcf or die "Can not open barcode file $bcf
+: $!\n";
while (my $line = <$barcodelist>) {
   chomp; 
   my ($id, $barcode) = split(/\t/,$line);
   # I like validating inputs
   warn "bad line at $.\n" unless $barcode =~/^[ACGT]+$/; 
   my $file = "$dir/sample_$barcode.fq";
   if (-e $file) {
     my $new = "$dir/$id.fq";
     rename $file, $new or die "Can't change $file to $new, $!\n";
   }
}
close $barcodelist;
[download]

Cheers,
R.

Thank you a lot, looks like the validation

 if (-e $file)

just makes the job

Can you try this version and report its output.

#!/usr/bin/perl
use strict;
use warnings;
opendir(DIR, "/samplesA") or die "Can not open folder, $!\n";
my @files = readdir(DIR);
closedir (DIR);
open my $barcodes, "<", "/ID.txt" or die "Can not open barcode file, $
+!\n";
my @lines=(<$barcodes>);
close $barcodes;

for my $file (@files) {
   next unless $file =~ m/fq$/;
   foreach my $line (@lines) {
      chomp $line;
      my ($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]

Perhaps strict and warnings will help

Cheers,
R.

Not, the strict and warning did not solve the problem, but I notice that when the folder contain few files (less than 20) the original scrip finish the job without problems. When the folder contain more files the original scrip stop working when it fund a file that does not have any barcode in the name. Any idea?

You forgot to chdir to that dir after that readdir you did to that dir :P

opendir is not for people :) people, its for computers

Path::Tiny is for people, as is glob and File::Find::Rule and ...

use Path::Tiny for working with paths. no readdir, readdir is too low-level, and too confusing for noobs (everybody who tried to use readdir even once)

also whitespace is for people

if ( -e $file ) {
  rename ($file, $new) or die "Can not change $file to $new, $!\n";
}
else {
  print "$file isn't there to be renamed $new\n";
}
[download]

The file exist and the scrip actually changes the name correctly, but I dont understand why, the scrip try to change the name again and of course, because it just changed the name of the file, the file does not exit any more. However the validation that you propose

 if ( -e $file )

allows the script finish the job, thank you

my $new = $file;
if ($new =~ s/sample_$barcode/$id/)
{
  rename ($file, $new) or die;
}
[download]

I tried it before, but it did not work. Thank you