Dear Monks, I basically have a long string of letters and I want to extract all letters between certain start and stop positions.

This works for me fine until the positions overlap (e.g. until the next start position is before the last stop position). There are up to three seperate start and stops per sequence as shown below.

Please can someone show me where i'm going wrong or suggest how to do this? My code is below, it fails to get things that overlap... Thanks!

foreach my $value (@data)   {
    # GET THE SEQUENCE FOR EACH $VALUE
    # STARTS AND STOPS ALSO DECLARED UP HERE
    # E.G. START1 =  1; START2 =  192; START3 = 600
    #      STOP1 = 280; STOP2 =  433; STOP3 = 753
    # Want to extract all letters between 1-280, 192-433 and 600-757 w
+here 280 and 192 overlap

# $sequence is a string with about 1000 letters

@seq = $sequence;
my $s = join ('', @seq);
@seq = split ('', $s);

 for (my $i=1; $i<=@seq; $i++)        {
        if (($i >= $start1) && ($i <= $stop1))  {
                push @current_seq, $seq[$i-1];
        }
        if ($i == $stop1)   {
                push @current_seq, "\n\n";
                      
        }
        if (($i >= $start2) && ($i <= $stop2))  {
                push @current_seq, $seq[$i-1];
        }
        if ($i == $stop2)       {
                push @current_seq, "\n\n";
        }
        if (($i >= $start3) && ($i <= $stop3))  {
                push @current_seq, $seq[$i-1];
                       }
        if ($i == $stop3)       {
                push @current_seq, "\n\n";
                     
        }

}
print "Sub-strings are:\n@current_seq\n";
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