<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>

CC BY-SA 4.0
2020-01-06T14:49:41.080Z
Welcome to the forum.  Can you add some context as to what this line is doing and why it answers the question?
Bioathlete
CC BY-SA 4.0
2020-01-03T22:39:24.113Z
2020-01-03T22:39:24.113Z
MdNazmulHossain
<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>

CC BY-SA 3.0
2018-02-09T17:10:10.243Z
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
Chris_Rands
CC BY-SA 3.0
2018-02-10T16:19:31.963Z
@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.
James
<phylogenetics><python><phylogeny>
How to find which scales are available in SeqUtil of Biopython?
# 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

Scalerefers to which scale being used. I am interested in how to give theScale` variable a valid variable.

The Biopython docs simply point out that there are many scales to choose from and the source code 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**: @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.  

---

## 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?  

---

