Hello, Biostars community I would like to receive your support with the next question.

I have developed this simple script to concatenate fasta sequences from different files in one single resulting file according to the same ID of each sequence respectively and It works, nevertheless, I would like to know if there is a way to control the order of the concatenation according to the name of the file.

For example

fie1_OTIB.fasta

seq1 aaa seq2 ccc

file2_OTIA.fasta

seq1 ttt seq2 ggg

file3_OTSS.fasta

seq1 ggg seq2 ttt

file4_OTLS

seq1 ccc seq2 aaa

For now, the script is going to give me this result in one fasta file

seq1 TTTAAAGGGCCC

Order for the seq1 >> file2 file1 file3 file4

seq2 GGGCCCTTTAAA

Order for the seq2 >> file2 file1 file3 file4

Here I would like to know if I could modify the script to order the concatenation according to my preference file due that, for now, it is taking a predetermined order, I would like in one case for example

seq1 AAATTTGGGCCC

ORDER = file1 file2 file3 file4

seq2 AAATTTGGGCCC

ORDER = file1 file2 file3 file4

Thanks in advance for your valuable support,

use Bio::SeqIO;

$input = "INPUT_DIRECTORY";
my %seqs;


        opendir DH, $input or die "Cannot open directory: $!";
        open (outfile, ">","OUTPUT_DIRECTOTY");

            while (my $file = readdir(DH)) {                                                    

                    next if $file =~ /^\./;                                                         
                    $new_file= $input."/".$file;
                    open GB, "$new_file" or die $!;

                my $seqio = Bio::SeqIO->new(-file => $new_file, -format => "fasta");

                while(my $seq = $seqio->next_seq) { 
                    my $seq_seq = $seq->seq();
                    my $seq_id = $seq->id();

                    $seqobj = Bio::Seq->new( -display_id => $seq_id, -seq => $seq_seq);
                    $seq_id = $seqobj->id();
                    $seqstr   = $seqobj->seq();
                    $seqs{$seqobj->display_id} .= $seqobj->seq;   

                }

            }

                foreach my $key (keys %seqs) { 
                        print outfile ">$key\n$seqs{$key}\n";
            }