title: Calculate percent identity between two already-aligned sequences
body: <p>I have two strings in a file like this:  </p>
  
  <pre><code>&gt;1
  atggca---------gtgtggcaatcggcacat
  &gt;2
  atggca---------gtgtggcaatcggcacat
  </code></pre>
  
  <p>Using the AlignIO function in Biopython:</p>
  
  <pre><code>from Bio import AlignIO
  print AlignIO.read("neighbor.fas", "fasta")
  </code></pre>
  
  <p>returns this:</p>
  
  <pre><code>SingleLetterAlphabet() alignment with 2 rows and 33 columns
  atggca---------gtgtggcaatcggcacat 1
  atggca---------gtgtggcaatcggcacat 2
  </code></pre>
  
  <p>I want to calculate the percentage identity between the two rows in this alignment.  </p>
  
  <pre><code>row = align[:,n]
  </code></pre>
  
  <p>allows for the extraction of individual columns that can be compared.  </p>
  
  <p>Columns that contain only "-" should not be counted.</p>