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  • Error in Biopython

    Newbie to Biopyton here....

    I'm getting the following error, from: can't read /var/mail/Bio.Seq, when I run the following at the terminal: from Bio.Seq import Seq

    I'm new to programming and VERY new to Biopython, so any help is greatly appreciated.

    Thanks in advance!

  • #2
    Originally posted by Kimist99 View Post
    Newbie to Biopyton here....

    I'm getting the following error, from: can't read /var/mail/Bio.Seq, when I run the following at the terminal: from Bio.Seq import Seq

    I'm new to programming and VERY new to Biopython, so any help is greatly appreciated.

    Thanks in advance!
    Make sure you're at the python prompt, >>> from Bio.Seq import Seq

    For all the Scientists turned Computational Biologists that asked questions obvious to CS folks.

    Comment


    • #3
      To expand on Kimist99's answer, you shouldn't run Python commands directly at the Unix terminal, e.g.

      Code:
      $ from Bio.Seq import Seq
      from: can't read /var/mail/Bio.Seq
      Here "$" is shorthand for the Unix terminal prompt, which usually ends with a dollar sign.

      This asked Unix to run the tool "from", which is command line tool for working with emails. You need to run Python first, and inside Python try the import line:

      Code:
      $ python
      Python 2.7.6 (default, Sep  9 2014, 15:04:36) 
      [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
      Type "help", "copyright", "credits" or "license" for more information.
      >>>
      That ">>>" is the Python prompt, where you could type a Python statement. e.g.

      Code:
      $ python
      Python 2.7.6 (default, Sep  9 2014, 15:04:36) 
      [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.39)] on darwin
      Type "help", "copyright", "credits" or "license" for more information.
      >>> from Bio.Seq import Seq
      >>> quit()
      You would typically create a text file whose name ends with ".py" containing your python script, e.g. "example.py", and run that at the Unix terminal with:

      Code:
      $ python example.py
      P.S. You might find my introductory Biopython workshop helpful: https://github.com/peterjc/biopython_workshop
      Last edited by maubp; 03-16-2015, 08:05 AM. Reason: adding link

      Comment


      • #4
        Agree with all of the above and highly recommend Anaconda. It is a completely free Python distribution (including for commercial use and redistribution). It includes over 195 of the most popular Python packages for science, math, engineering, data analysis. http://continuum.io/downloads

        Spend five minutes to get used to IPython and the notebook and your life will be so much easier!
        LM

        Comment


        • #5
          shimbalama-- thanks for the info. That's helpful!

          Comment

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