Control concatenation order in a fasta file

Question

[Damian_Civ]

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 = "FOLDER_INPUT_FASTA_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";
}

[cpad0112]

do all the files have same number of sequences? Damian_Civ. Try seqkit concat. It concatenates as per ID and file name order.

[Nitin Narwade]

In your code, opendir will get the directory content in sorted order.

As you mentioned if the names of the files are exactly the same as fie1_OTIB.fasta, file2_OTIA.fasta, file3_OTSS.fasta, file4_OTLS then you will get output as your expecting but if the file names are without file(number)_ prefix then opendir will get the directory content in a different order like OTIA.fasta, OTIB.fasta, OTLS.fasta, OTSS.fasta and your output will be file2 file1 file4 file3.

If this is the problem then renaming the files in lexicographical order would be a dummy solution.

Thanks.