Answers.Body: <p>Use this line of code:    </p>
  
  <pre><code>print(analysed_seq.protein_scale(analysed_seq.get_amino_acids_percent(), window=9, edge=0.4))
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-06T14:49:41.080Z
Answers.Text: Welcome to the forum.  Can you add some context as to what this line is doing and why it answers the question?
Answers.UserDisplayName: Bioathlete
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-03T22:39:24.113Z
Answers.LastActivityDate: 2020-01-03T22:39:24.113Z
Answers.UserDisplayName: MdNazmulHossain
Body: <p>I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil".</p>
  
  <pre><code>analysed_seq = ProteinAnalysis("AKVLGSLEALEPVHYEEKNWCE")
  analysed_seq.protein_scale(Scale, WindowSize, Edge)
  </code></pre>
  
  <p><strong>Known parameters</strong></p>
  
  <ul>
  <li><code>WindowSize</code> refers to the total number of amino acids to be considered either side of the residue (an <code>int</code> variable). </li>
  <li><code>Edge</code> refers to the weighting of the scale further from the centre of the window (0-1). `</li>
  </ul>
  
  <p><strong>Unknown parameter</strong></p>
  
  <ul>
  <li>Scale<code>refers to which scale being used. I am interested in how to give the</code>Scale` variable a valid variable.</li>
  </ul>
  
  <p>The <a href="http://biopython.org/wiki/ProtParam" rel="nofollow noreferrer">Biopython docs</a> simply point out that there are many <code>scales</code> to choose from and the <a href="http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis.protein_scale" rel="nofollow noreferrer">source code</a> doesn't seem to give any clues about scale options.</p>
  
  <p>Where can I find a list of the <code>scale</code> are available and how to call them?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-09T17:10:10.243Z
Comments.Text: what do you mean? There is no scale argument to feed `protein_scale()` only `def protein_scale(self, param_dict, window, edge=1.0):` https://github.com/biopython/biopython/blob/master/Bio/SeqUtils/ProtParam.py#L211. I think `param_dict` is `kd` https://github.com/biopython/biopython/blob/master/Bio/SeqUtils/ProtParamData.py#L6
Comments.UserDisplayName: Chris_Rands
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2018-02-10T16:19:31.963Z
Comments.Text: @Chris_Rands You've answered the question, thanks. I was looking for any predefined `param_dict` arguments and the GitHub source code spells them out clearly. It also looks like you can feed a scale straight in without having to edit `ProtParamsData` which satisfies me more.
Comments.UserDisplayName: James
Tags: <phylogenetics><python><phylogeny>
Title: How to find which scales are available in SeqUtil of Biopython?
ThreadText: # How to find which scales are available in SeqUtil of Biopython?
  
  (Asked by: username_0 on 2018-02-09)
  
  I am trying to analyse the hydrophobicity of a sequence using BioPython's "SeqUtil".
  
  ```
  analysed_seq = ProteinAnalysis("AKVLGSLEALEPVHYEEKNWCE")
  analysed_seq.protein_scale(Scale, WindowSize, Edge)
  
  ```
  
  **Known parameters**
  
  * `WindowSize` refers to the total number of amino acids to be considered either side of the residue (an `int` variable).
  * `Edge` refers to the weighting of the scale further from the centre of the window (0-1). `
  
  **Unknown parameter**
  
  * Scale`refers to which scale being used. I am interested in how to give the`Scale` variable a valid variable.
  
  The [Biopython docs](http://biopython.org/wiki/ProtParam) simply point out that there are many `scales` to choose from and the [source code](http://biopython.org/DIST/docs/api/Bio.SeqUtils.ProtParam-pysrc.html#ProteinAnalysis.protein_scale) doesn't seem to give any clues about scale options.
  
  Where can I find a list of the `scale` are available and how to call them?
  
  **Tags:** phylogenetics, python, phylogeny
  
  > **Comments:**
  > **username_1**: what do you mean? There is no scale argument to feed `protein_scale()` only `def protein_scale(self, param_dict, window, edge=1.0):` https://github.com/biopython/biopython/blob/master/Bio/SeqUtils/ProtParam.py#L211. I think `param_dict` is `kd` https://github.com/biopython/biopython/blob/master/Bio/SeqUtils/ProtParamData.py#L6  
  > **username_0**: @username_1 You've answered the question, thanks. I was looking for any predefined `param_dict` arguments and the GitHub source code spells them out clearly. It also looks like you can feed a scale straight in without having to edit `ProtParamsData` which satisfies me more.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-01-03. Score: 1
  
  Use this line of code:
  
  ```
  print(analysed_seq.protein_scale(analysed_seq.get_amino_acids_percent(), window=9, edge=0.4))
  
  ```
  
  > **Comments:**
  > **username_3**: Welcome to the forum.  Can you add some context as to what this line is doing and why it answers the question?  
  
  ---
  
  