#!/usr/bin/perl 

#use strict;
#use warnings;

my $sourceDir = '../Perl/Test';
my $outFile = "out.ffn";
my $i = 0;


opendir(my $sourceDH, $sourceDir) or die $!;
my @allfiles = grep /\.ffn$/, sort readdir($sourceDH);
closedir $sourceDH;


open my $outFH, ">>", $outFile or die $!;

for my $sourceFile (@allfiles) {
    
   
    open my $sourceFH, "<", $sourceDir . '/' . $sourceFile or die $!;
        
    $NameReadIn = <$sourceFH>; 
    
        close $sourceFH;

# Get organism name 

chop($NameReadIn);
$NameReadIn =~s/(>)/_/g;
$NameReadIn =~s/(\[)/>/g;

        $positionName=index($NameReadIn,">");
        $ZeichenName = substr($NameReadIn,$positionName,);
        chop($Name);

if ( -z "$outFH" ) 
        {
         print $outFH "$Name\n";
        }

else    {
        print $outFH "\n$Name\n";
        }

# Get sequences:

    open my $sourceFH, "<", $sourceDir . '/' . $sourceFile or die $!;
        
        @DNAReadIn  = <$sourceFH>;              

        close $sourceFH;

$DNAString=join("",@DNAReadIn);
$DNAString =~s/(\]\n)/,/g;


while ($DNAString =~ m{,\w{3}(\w{24})}g)
 
        {
        print $outFH "$1";
        }

$i++;

}

close $outFH;

print "Done! $i files have been processed!\n";