# set up chromosome sequence object
my $file = $chromosome.'.fa';
my $seqio = Bio::SeqIO->new(
	-format	=> 'largefasta',
	-file	=> $file
	);

# set up range parameters
my $strand = '+';
my $seq_start = 1_000_000;
my $seq_end   = 2_000_000;
my $downstream= 10_000;

# handle sequences on both strands
if ($strand eq '+') {
	$seq_start = $tx_start - $upstream;
	$seq_end   = $tx_start + $downstream;
	if ($seq_start < 0) { next(); }
	if ($seq_end > $length) { next(); }
	$seq_mRNA  = $seq_chr->trunc($seq_start,$seq_end);
	}
elsif ($strand eq '-') {
	$seq_start = $tx_end + $upstream;
	$seq_end   = $tx_end - $downstream;
	if ($seq_end < 0) { next(); }
	if ($seq_start > $length) { next(); }
	$seq_mRNA  = $seq_chr->trunc($seq_end,$seq_start)->revcom();
	}
else {
	warn "No strand: $strand!\n";
	next();
	}

# write seq to a file
my $outfile = $mRNA.'.fasta';
open(OUT, '>', $outfile);
print OUT ">$mRNA\n", $seq_mRNA->seq();
close(OUT);