Answers.Body: <p>When the user is pushing <code>enter</code> on their keyboard, it is likely inserting a newline character (<code>\n</code>) at the end of the user input <code>entry</code> and causing the error you have included in your question. You can strip the <code>\n</code> by using <code>entry.rstrip('\n')</code>:</p>
  <pre class="lang-py prettyprint-override"><code># entry - user inputted string taking in amino acid letters
  entry = e1.get()
  entry = entry.rstrip('\n')
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  </code></pre>
  <hr />
  <p>From the comments where the <code>print(entry)</code> was given as</p>
  <blockquote>
  <p><code>MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN</code></p>
  </blockquote>
  <p>and <code>print(repr(entry))</code> is given as</p>
  <blockquote>
  <p><code>'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG\nGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'</code></p>
  </blockquote>
  <p>the <code>\n</code> character is not at the end of the line so <code>.rstrip('\n')</code> cannot be used (it only works at the end of the string).</p>
  <p>Try instead <code>.replace('\n', '')</code>:</p>
  <pre class="lang-py prettyprint-override"><code># entry - user inputted string taking in amino acid letters
  entry = e1.get()
  entry = entry.replace('\n', '')
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  </code></pre>
  <p>which on my system (removing the <code>prot_data</code> and <code>result</code> lines) outputs without the <code>\n</code> character and <code>print(repr(entry))</code> is the same as <code>print(entry)</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-06-20T00:59:57.533Z
Answers.Text: @Z_Gonzalez rightttt, it's in the middle of the string, I just assumed as it was user input the `\n` was at the end, `.rstrip()` only works from the end of the string, we need to use `.replace()` instead, will edit the answer shortly
Answers.UserDisplayName: piJT
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-06-19T12:05:50.020Z
Answers.LastActivityDate: 2023-06-20T16:16:41.647Z
Answers.LastEditDate: 2023-06-20T16:16:41.647Z
Answers.UserDisplayName: piJT
Body: <p>I am trying to run a function from the ProtParam script in the Bio.SeqUtils package. The function is for calculating the instability index of a protein. The code I am using in my script with the pre-built function is the following:</p>
  <pre><code># entry - user inputted string taking in amino acid letters
  entry = e1.get()
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  </code></pre>
  <p>When I run the code, I get the following key error related to the instability_index function.</p>
  <pre><code>File &quot;/Genome_Toolkit/venv/lib/python3.9/site- packages/Bio/SeqUtils/ProtParam.py&quot;, line 152, in instability_index
  dipeptide_value = index[this][next]
  KeyError: '\n'
  </code></pre>
  <p>The instability_index() function in the ProtParam script looks like this:</p>
  <pre><code>def instability_index(self):
      index = ProtParamData.DIWV
      score = 0.0
  
      for i in range(self.length - 1):
          this, next = self.sequence[i: i + 2]
          dipeptide_value = index[this][next]
          score += dipeptide_value
  
      return (10.0 / self.length) * score
  </code></pre>
  <p>I looked at the script myself, specifically the line the error is referring to but couldn't pinpoint the issue. Any guidance is appreciated. Thanks!</p>
  <p>the output of <code>print(entry)</code> and <code>print(repr(entry))</code> looks like this, which is exactly what the entry was in the input:</p>
  <pre><code>MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
  GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
  'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG\nGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'
  </code></pre>
  
Tags: <proteins><errors><biopython>
Title: KeyError '/n' in Bio SeqUtils Package ProtParam Script
ThreadText: # KeyError '/n' in Bio SeqUtils Package ProtParam Script
  
  (Asked by: username_0 on 2023-06-18)
  
  I am trying to run a function from the ProtParam script in the Bio.SeqUtils package. The function is for calculating the instability index of a protein. The code I am using in my script with the pre-built function is the following:
  
  ```
  # entry - user inputted string taking in amino acid letters
  entry = e1.get()
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  
  ```
  
  When I run the code, I get the following key error related to the instability\_index function.
  
  ```
  File "/Genome_Toolkit/venv/lib/python3.9/site- packages/Bio/SeqUtils/ProtParam.py", line 152, in instability_index
  dipeptide_value = index[this][next]
  KeyError: '\n'
  
  ```
  
  The instability\_index() function in the ProtParam script looks like this:
  
  ```
  def instability_index(self):
      index = ProtParamData.DIWV
      score = 0.0
  
      for i in range(self.length - 1):
          this, next = self.sequence[i: i + 2]
          dipeptide_value = index[this][next]
          score += dipeptide_value
  
      return (10.0 / self.length) * score
  
  ```
  
  I looked at the script myself, specifically the line the error is referring to but couldn't pinpoint the issue. Any guidance is appreciated. Thanks!
  
  the output of `print(entry)` and `print(repr(entry))` looks like this, which is exactly what the entry was in the input:
  
  ```
  MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG
  GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN
  'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG\nGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'
  
  ```
  
  **Tags:** proteins, errors, biopython
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2023-06-19. Score: 3 | Accepted answer
  
  When the user is pushing `enter` on their keyboard, it is likely inserting a newline character (`\n`) at the end of the user input `entry` and causing the error you have included in your question. You can strip the `\n` by using `entry.rstrip('\n')`:
  
  ```py
  # entry - user inputted string taking in amino acid letters
  entry = e1.get()
  entry = entry.rstrip('\n')
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  
  ```
  
  ---
  
  From the comments where the `print(entry)` was given as
  
  > `MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG GPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN`
  
  and `print(repr(entry))` is given as
  
  > `'MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHLVEALYLVCGERGFFYTPKTRREAEDLQVGQVELGG\nGPGAGSLQPLALEGSLQKRGIVEQCCTSICSLYQLENYCN'`
  
  the `\n` character is not at the end of the line so `.rstrip('\n')` cannot be used (it only works at the end of the string).
  
  Try instead `.replace('\n', '')`:
  
  ```py
  # entry - user inputted string taking in amino acid letters
  entry = e1.get()
  entry = entry.replace('\n', '')
  prot_data = ProteinAnalysis(entry)
  result = prot_data.instability_index()
  
  ```
  
  which on my system (removing the `prot_data` and `result` lines) outputs without the `\n` character and `print(repr(entry))` is the same as `print(entry)`.
  
  > **Comments:**
  > **username_1**: @username_0 rightttt, it's in the middle of the string, I just assumed as it was user input the `\n` was at the end, `.rstrip()` only works from the end of the string, we need to use `.replace()` instead, will edit the answer shortly  
  
  ---
  
  