#!/usr/bin/perl -w
use warnings;
use warnings FATAL => q{void};
use warnings FATAL => 'syntax';
use strict;
use Data::Dumper; 

print "Enter your chromosome";
my $chromosome = <STDIN>;
chomp $chromosome;

print "Your file is '$chromosome'\n";
# reading whole file
$file_name = $ARGV[0];
open(my $file, '<', $file_name) or die "Sorry, we can't open your $file_name $!";
@content= <$file>;
close $file;
print "\n\n";
$index_max = $#content;
for ($start=0; $start <= $index_max; $start++)
{
    chomp $content[$i];
    print "Reg $i: $content[$i]\n";

    if ($content[$start] =~ /CDS/ )
    {
        print "There is CDS \n";
        for ($start;$start <= $index_max; $start++)
        {
            @cds = (@cds, $content[$start]);
            print @cds;
        }
        open (WRITE, ">>concatenare.txt");
        print WRITE @cds;
        close WRITE;
    }
    #This chromosome have tags. Identify CDS ones.
    my @features =$mySeq ->all_seqfeatures();
    foreach $feature (@features)
    {
        my @tag = $CDS;
        my @feat = $join;
        foreach $tag ( $feat->all tags() );
        print "Feature region has tag", $tag, "CDS",
        join(‘ ‘,$feat->each tag value($tag)), "\n";
    }

    if ($content[$start] =~ /ORIGIN/ )
    {
        print "There is ORIGIN !! \n";
        for ($start;$start <= $index_max; $start++)
        {
        @origin = (@origin, $content[$start]);
        shift (@origin); #Delete ORIGIN row;
        print @origin;
        for @origin
        {
while ($_ =~ m/[ACGTURYKMSWBDHVN]/ig)
    {

        $seq = $seq.$&;
    }
}
$lenght = length($seq);
print "The sequence has $nucleotide length\n";
print "$seq";
        }
    }
}
print "There is ",$index_max," inregistrari\n";
print "This are:\n\n";

my $file = "concatenare.txt";
my $succ = open( my $fh , '>>', $file );

$fh = *STDOUT unless $succ;

print $fh "CDS1 \n";
print $fh "Nucleotide sequence \n";
print $fh "CDS2 \n";
print $fh "Nucleotide sequence \n";