title: perl file manipulation
body: <p>I have a file <strong>File1</strong> that contains these data : </p>
  
  <pre><code>NC_009066   5239    5308    trnA(tgc)   2.10899859667e-09   -
  NC_009066   5309    5382    trnN(gtt)   7.03000463545e-10   -
  NC_009066   5422    5487    trnC(gca)   7.09999799728e-08   -
  NC_009066   5487    5557    trnY(gta)   3.72200156562e-11   -
  NC_009066   5549    7097    cox1    291081744.81    +
  NC_009066   7109    7180    trnS2(tga)  1.83000043035e-09   -
  NC_009066   7183    7256    trnD(gtc)   2.5720000267e-09    +
  </code></pre>
  
  <p>and another fasta file <strong>File2</strong> </p>
  
  <pre><code>&gt; NC_009066,1,0-17045,
  GCTATCGTAGCTTAATTAAAGCATAACACTGAAGATGTTAAGATGAACCCTAGAAA
  </code></pre>
  
  <p>I've put the file1 in an array line by line and then i can access each column by splitting each line on <code>/\s+/</code>. </p>
  
  <pre><code>for $line(@array){
      @column= split(/\s+/,$line);
      # print $column[5]."\n";
  
  $gene=substr($seq,$column[1],$column[2]);#$seq extracted from File2....}
  </code></pre>
  
  <p>but I want to do is to take the second column from the 1st line with the 3rd column from the 2nd line <code>(substr($seq,5239,5382))</code> and then 2nd column from 2nd line and 3rd column from 3rd line <code>(substr($seq,5309,5487))</code>.....
  what is the best way to do it ?? </p>