title: Python script running header from interpreter
body: <h2>Noob warning</h2>
  <p>I have a script I'm trying to run (<code>rename_oturep.py</code>) in the cmd prompt. When I run <code>python rename_oturep.py</code> I get this error:</p>
  <pre class="lang-py prettyprint-override"><code>File &quot;rename_oturep.py&quot;, line 1
      Python 3.8.0 (tags/v3.8.0:fa919fd, Oct 14 2019, 19:37:50) [MSC v.1916 64 bit (AMD64)] on win32
             ^
  SyntaxError: invalid syntax
  </code></pre>
  <p>So, it seems the script is reading from the header from the interpreter when I try to run that script.</p>
  <p>E.g.</p>
  <p>Input:</p>
  <pre><code>X:\Python 3.8&gt; python
  </code></pre>
  <p>Output:</p>
  <pre class="lang-py prettyprint-override"><code>Python 3.8.0 (tags/v3.8.0:fa919fd, Oct 14 2019, 19:37:50) [MSC v.1916 64 bit (AMD64)] on win32
  Type &quot;help&quot;, &quot;copyright&quot;, &quot;credits&quot; or &quot;license&quot; for more information.
  </code></pre>
  <p>I have deleted the header info in IDLE &amp; honestly have no idea why it is reading the interpreter header as part of the script. I have run this script successfully before (a couple of weeks ago) with no issues. Why is this just now an issue? Anyone have a similar experience?</p>
  <p>Here is the actual script code (copypasta direct from IDLE):</p>
  <pre class="lang-py prettyprint-override"><code>import sys
  
  import re
  
  
  info = []
  
  
  with open(sys.argv[1], 'r') as fasta_in:
      for line in fasta_in:
          info.append(line.replace('\r', '').rstrip('\n'))
  
  
  seqs = []
  
  list
  for index, item in enumerate(info):
      if index == 0:
          ID = re.search('Otu[0-9]*',item[1:]).group(0)
      else:
          if index % 2 == 0:
              ID = re.search('Otu[0-9]*',item[1:]).group(0)
          else:
              seqs.append((ID, item))
  
  
  with open(&quot;clean_repFasta.fasta&quot;, 'w') as fasta_out:
      for item in seqs:
          fasta_out.write('&gt;' + item[0] + '\n' + item[1] + '\n')
  </code></pre>