#!/usr/bin/perl

($root,$gene) = (@ARGV);
open(TXT,$root.".txt") || die "Cannot open $root.txt";
open(FASTA, $root.".fasta") || die "Cannot open $root.fasta";

$found=0;
while (<TXT>) { 
    ($start,$stop) = m/^$gene \((\d+)..(\d+)\)/io || next;
    $found=1; 
    last;
}
die "Did not find gene $gene in $root.txt" unless $found=1;

$found = 0;
while (<FASTA>) { 
  chop; 
  @x=split;
  if ($x[0] >= $start) { 
      # start-logic here;
  }
}
while (<FASTA>) { 
  chop; 
  @x=split;
  if ($x[0] <= $stop) { 
      # stop-logic here
  }
}
# print logic here


##</code><code>##

    rps12       -(92301..93101)
	rps7        -(91772..92242)
	ndhB        -(89236..91472)
	trnL        -(88584..88664)
	trnI        -(84881..84954)
	rpl23       -(84433..84714)
	rpl2        -(82930..84414)


##</code><code>##

http://www.ncbi.nlm.nih.gov/nuccore/11994090?report=fasta&log$=seqview