Answers.Body: <p>You are trying to run a script file in the python console. That doesn't make sense. The console is for running commands manually, interactively. A script is a collection of commands. You can't just run that by name in the console. If you want to use it, copy the <em>contents</em> of your script and try to run them in the console. </p>
  
  <p>The way you run a python <em>script file</em> is simply:</p>
  
  <pre><code>python vcf2maf.py -h
  </code></pre>
  
  <p>Or, assuming you have made the file executable and it has the right <a href="https://en.wikipedia.org/wiki/Shebang_(Unix)" rel="nofollow noreferrer">shebang line</a>, just:</p>
  
  <pre><code>./vcf2maf.py -h
  </code></pre>
  
  <hr>
  
  <p>The specific error you are getting is because <code>foo.bar</code> in Python means "run the <code>bar</code> method from the object <code>foo</code>. So <code>vcf2maf.py</code> means run <code>py</code> from <code>vcf2maf</code>. Since there is no object defined with the name <code>vcf2maf</code>, you get the <code>name 'vcf2maf' is not defined</code>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-01T12:03:47.543Z
Answers.Text: Sorry says that Last login: Wed Apr  1 11:50:14 on ttys000
  pc-133-235:~ fi1d18$ pwd
  /Users/fi1d18
  pc-133-235:~ fi1d18$ 
  pc-133-235:~ fi1d18$ cd Downloads
  pc-133-235:Downloads fi1d18$ python vcf2maf.py -h
  Traceback (most recent call last):
    File "vcf2maf.py", line 19, in <module>
      import vcf
  ImportError: No module named vcf
  pc-133-235:Downloads fi1d18$
Answers.UserDisplayName: Zizogolu
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-01T12:26:35.417Z
Answers.Text: @Angel I can't read that. Please [edit] your question to add extra information, don't put it in the comments. And tell me who/what "says" and when. I can't guess what commands you are running. If that's the output of running the script, then it is a completely different issue, you are missing the `vcf` module. So please ask a new question about that.
Answers.UserDisplayName: terdon
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-04-01T11:53:52.413Z
Answers.LastActivityDate: 2020-04-01T11:53:52.413Z
Answers.UserDisplayName: terdon
Body: <p>I am trying to run a script in python but I getting this error</p>
  
  <pre><code>loan-mac-13:vcf2maf fi1d18$ python
  Python 2.7.10 (default, Feb 22 2019, 21:55:15) 
  [GCC 4.2.1 Compatible Apple LLVM 10.0.1 (clang-1001.0.37.14)] on darwin
  Type "help", "copyright", "credits" or "license" for more information.
  &gt;&gt;&gt; import os
  &gt;&gt;&gt; os.chdir("/Users/fi1d18/Downloads/vcf2maf-master/vcf2maf")
  &gt;&gt;&gt; 
  &gt;&gt;&gt; 
  &gt;&gt;&gt; os.getcwd()
  '/Users/fi1d18/Downloads/vcf2maf-master/vcf2maf'
  &gt;&gt;&gt; vcf2maf.py -h
  Traceback (most recent call last):
    File "&lt;stdin&gt;", line 1, in &lt;module&gt;
  NameError: name 'vcf2maf' is not defined
  &gt;&gt;&gt; python vcf2maf.py -h
    File "&lt;stdin&gt;", line 1
      python vcf2maf.py -h
                   ^
  SyntaxError: invalid syntax
  &gt;&gt;&gt; 
  </code></pre>
  
  <p>Where I am doing wrong?</p>
  
  <p>Thanks for any help</p>
  
  <p>By your comments I run</p>
  
  <p>Sorry says that Last login: Wed Apr  1 11:50:14 on ttys000</p>
  
  <pre><code>pc-133-235:~ fi1d18<span class="math-container">$ pwd
  /Users/fi1d18
  pc-133-235:~ fi1d18$</span> 
  pc-133-235:~ fi1d18<span class="math-container">$ cd Downloads
  pc-133-235:Downloads fi1d18$</span> python vcf2maf.py -h
  Traceback (most recent call last):
    File "vcf2maf.py", line 19, in &lt;module&gt;
      import vcf
  ImportError: No module named vcf
  pc-133-235:Downloads fi1d18$
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-01T15:52:29.190Z
Comments.Text: As I said, that's a completely separate issue. Please ask a new question about it. First, however, just copy/paste the error into your favorite search engine. That will give you the answer.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-04T13:22:47.140Z
Comments.Text: I am sorry to say, but this is a bioinformatics equivalent of "What is a cell" in biology. It appears to me that you really should go through some python tutorials to get over the basics before you proceed with your research. I heavily recommend https://software-carpentry.org/ as a starting point.
Comments.UserDisplayName: Kamil S Jaron
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-04-04T15:10:11.237Z
Comments.Text: You %100 right @KamilSJaron, I am nothing in the first line of python
Comments.UserDisplayName: Zizogolu
Tags: <python><vcf><software-usage>
Title: Running a script in python
ThreadText: # Running a script in python
  
  (Asked by: username_0 on 2020-04-01)
  
  I am trying to run a script in python but I getting this error
  
  ```
  loan-mac-13:vcf2maf fi1d18$ python
  Python 2.7.10 (default, Feb 22 2019, 21:55:15) 
  [GCC 4.2.1 Compatible Apple LLVM 10.0.1 (clang-1001.0.37.14)] on darwin
  Type "help", "copyright", "credits" or "license" for more information.
  >>> import os
  >>> os.chdir("/Users/fi1d18/Downloads/vcf2maf-master/vcf2maf")
  >>> 
  >>> 
  >>> os.getcwd()
  '/Users/fi1d18/Downloads/vcf2maf-master/vcf2maf'
  >>> vcf2maf.py -h
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
  NameError: name 'vcf2maf' is not defined
  >>> python vcf2maf.py -h
    File "<stdin>", line 1
      python vcf2maf.py -h
                   ^
  SyntaxError: invalid syntax
  >>> 
  
  ```
  
  Where I am doing wrong?
  
  Thanks for any help
  
  By your comments I run
  
  Sorry says that Last login: Wed Apr 1 11:50:14 on ttys000
  
  ```
  pc-133-235:~ fi1d18$ pwd
  /Users/fi1d18
  pc-133-235:~ fi1d18$ 
  pc-133-235:~ fi1d18$ cd Downloads
  pc-133-235:Downloads fi1d18$ python vcf2maf.py -h
  Traceback (most recent call last):
    File "vcf2maf.py", line 19, in <module>
      import vcf
  ImportError: No module named vcf
  pc-133-235:Downloads fi1d18$
  
  ```
  
  **Tags:** python, vcf, software-usage
  
  > **Comments:**
  > **username_1**: As I said, that's a completely separate issue. Please ask a new question about it. First, however, just copy/paste the error into your favorite search engine. That will give you the answer.  
  > **username_2**: I am sorry to say, but this is a bioinformatics equivalent of "What is a cell" in biology. It appears to me that you really should go through some python tutorials to get over the basics before you proceed with your research. I heavily recommend https://software-carpentry.org/ as a starting point.  
  > **username_0**: You %100 right @username_2, I am nothing in the first line of python  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2020-04-01. Score: 4 | Accepted answer
  
  You are trying to run a script file in the python console. That doesn't make sense. The console is for running commands manually, interactively. A script is a collection of commands. You can't just run that by name in the console. If you want to use it, copy the *contents* of your script and try to run them in the console.
  
  The way you run a python *script file* is simply:
  
  ```
  python vcf2maf.py -h
  
  ```
  
  Or, assuming you have made the file executable and it has the right [shebang line](https://en.wikipedia.org/wiki/Shebang_(Unix)), just:
  
  ```
  ./vcf2maf.py -h
  
  ```
  
  ---
  
  The specific error you are getting is because `foo.bar` in Python means "run the `bar` method from the object `foo`. So `vcf2maf.py` means run `py` from `vcf2maf`. Since there is no object defined with the name `vcf2maf`, you get the `name 'vcf2maf' is not defined`.
  
  > **Comments:**
  > **username_0**: Sorry says that Last login: Wed Apr  1 11:50:14 on ttys000 pc-133-235:~ fi1d18$ pwd /Users/fi1d18 pc-133-235:~ fi1d18$  pc-133-235:~ fi1d18$ cd Downloads pc-133-235:Downloads fi1d18$ python vcf2maf.py -h Traceback (most recent call last):   File "vcf2maf.py", line 19, in <module>     import vcf ImportError: No module named vcf pc-133-235:Downloads fi1d18$  
  > **username_1**: @Angel I can't read that. Please [edit] your question to add extra information, don't put it in the comments. And tell me who/what "says" and when. I can't guess what commands you are running. If that's the output of running the script, then it is a completely different issue, you are missing the `vcf` module. So please ask a new question about that.  
  
  ---
  
  