in reply to Perl script for concatenating multiple files in aspecific order listed in a txt file

Hello Anonymous Monk,

I see already the fellow Monks have provided you with plenty of options. I just would like to provide two more possible solutions.

But I still lost, what is the a specific order of the files in your file? Is it in numerical order?

Since you did not provide us with an example of your file and expected output I will just assume, and propose something. Why not extract all FASTA files from the file in an array and simply concatenate them with the join?

Just a suggestion if I have understand correctly.

Provide us more information so we can help you.

Solution one using File::Slurp/read_dir:

#! /usr/bin/perl
use strict;
use warnings;
use File::Slurp;
use Data::Dumper;

my $dir = '.';

my @files = read_dir($dir);

@files = sort @files;

@files = grep {$_ ne '.' && $_ ne '..'} @files;

print Dumper \@files;

__END__

$ perl test.pl
$VAR1 = [
          'test.pl',
          'test.pl~',
          'test_1.txt',
          'test_2.txt',
          'test_2a.txt',
          'test_2b.txt',
          'test_2c.txt',
          'test_3.txt'
        ];

[download]

Solution two using readdir:

#! /usr/bin/perl
use strict;
use warnings;
use Data::Dumper;

my $dir = '.';

opendir( my $dh, $dir)
    or die "Cannot open ".$dir." - $!";

my @files = sort readdir($dh);

@files = grep {$_ ne '.' && $_ ne '..'} @files;

closedir $dh
    or warn "Cannot close ".$dir." - $!";

print Dumper \@files;

__END__

$ perl test.pl
$VAR1 = [
          'test.pl',
          'test.pl~',
          'test_1.txt',
          'test_2.txt',
          'test_2a.txt',
          'test_2b.txt',
          'test_2c.txt',
          'test_3.txt'
        ];

[download]

Sorry I miss understood the question.

Looking forward to your update, BR.

Seeking for Perl wisdom...on the process of learning...not there...yet!
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