text: user747: I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window does not have 20 values.
  from Bio.SeqUtils.ProtParam import ProteinAnalysis
  
  window_length=20
  edge=1
  kyte = {'A': 1.8, 'R': -4.5, 'N': -3.5, 'D': -3.5, 'C': 2.5, 'Q': -3.5, 'E': -3.5, 'G': -0.4, 'H': -3.2, 'I': 4.5,
          'L': 3.8, 'K': -3.9, 'M': 1.9, 'F': 2.8, 'P': -1.6, 'S': -0.8, 'T': -0.7, 'W': -0.9, 'Y': -1.3, 'V': 4.2}
  
  full_sequence_analysis = ProteinAnalysis("CYGTGAVYLLGLGIGGFS")
  kyte_window = full_sequence_analysis.protein_scale(kyte, window_length, edge)
  
  Is there are a built in Biopython option in this for "allow half windows/short windows" for incomplete windows? There is nothing I can see to suggest so in the docs.
  
  user6244: You can choose between a window_size of 20 for sequences longer than 20 AAs, and the length of the sequence for those shorter::
  seq = "CYGTGAVYLLGLGIGGFS"
  window_length = min(len(seq), 20)
  
  full_sequence_analysis = ProteinAnalysis(seq)
  kyte_window = full_sequence_analysis.protein_scale(kyte, window_length, edge)
  
  
original_text: 747: <p>I am using Biopython to examine protein sequences including the Kyte and Doolittle hydrophobicity. However, for short sequences, this returns an empty value; the value is not allowed if the window does not have 20 values.</p>
  
  <pre><code>from Bio.SeqUtils.ProtParam import ProteinAnalysis
  
  window_length=20
  edge=1
  kyte = {'A': 1.8, 'R': -4.5, 'N': -3.5, 'D': -3.5, 'C': 2.5, 'Q': -3.5, 'E': -3.5, 'G': -0.4, 'H': -3.2, 'I': 4.5,
          'L': 3.8, 'K': -3.9, 'M': 1.9, 'F': 2.8, 'P': -1.6, 'S': -0.8, 'T': -0.7, 'W': -0.9, 'Y': -1.3, 'V': 4.2}
  
  full_sequence_analysis = ProteinAnalysis("CYGTGAVYLLGLGIGGFS")
  kyte_window = full_sequence_analysis.protein_scale(kyte, window_length, edge)
  </code></pre>
  
  <p>Is there are a built in Biopython option in this for "allow half windows/short windows" for incomplete windows? There is nothing I can see to suggest so in <a href="http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis.protein_scale" rel="nofollow noreferrer">the docs</a>.</p>
   6244: <p>You can choose between a <code>window_size</code> of 20 for sequences longer than 20 AAs, and the length of the sequence for those shorter::</p>
  
  <pre><code>seq = "CYGTGAVYLLGLGIGGFS"
  window_length = min(len(seq), 20)
  
  full_sequence_analysis = ProteinAnalysis(seq)
  kyte_window = full_sequence_analysis.protein_scale(kyte, window_length, edge)
  </code></pre>
  