hello! becuase you mentioned about "CDS", "original", so I guess you want parser information from a genbank format file, right? (e.g. https://www.ncbi.nlm.nih.gov/nuccore/M85050.1) as cavac say, if you do not offer file format, other people can't understand what do you want to do, and then understand wether the code work good. so I can't offer how to make your code work correctly, too.

there are some part of your maybe need change, I just try to give some advice:)

            @cds = (@cds, $content[$start]);
            print @cds;
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before this paragraph, @cd did not defined in anywher, so this will make script stop work, and because it assigned by itself, I can't understand purpose of this statements, so I don't know how to modify it, but I sure it won't work now.

       for ($start;$start <= $index_max; $start++)
        {
        @origin = (@origin, $content[$start]);
        shift (@origin); #Delete ORIGIN row;
        print @origin;
        for @origin
        {
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this part have same problem, what is @origin?

   #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";
    }
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I guess you defined subroutines in other site, so I don't what can they do, ;-;.

open(my $file, '<', $file_name) or die "Sorry, we can't open your $fil
+;
open (WRITE, ">>concatenare.txt");
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you used two style of open() in this code, first is better, please use it every times.

you can use  while(my $line = <$fh>){...}, this will read one line of file in each times. so you don't need read all content into a array, and don't need to find the last index before. if you actually treat a very big file, it will reduce ram occupied by program.

p.s. yes, Bioperl can resolve most of problem.