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  • Unable to install biopython on windows properly

    Hi,

    I tried installing biopython 1.64 on my windows computer. Python version I use is - 3.3.4. I installed numpy1.8.2 too. When I check how they are working(according to the installation pdf obtained from the biopython site) it gives me the following errors. How can this be solved?

    >>> import Bio
    >>> print(Bio._version_)
    Traceback (most recent call last):
    File "<pyshell#1>", line 1, in <module>
    print(Bio._version_)
    AttributeError: 'module' object has no attribute '_version_'
    >>> from Numeric import *
    Traceback (most recent call last):
    File "<pyshell#2>", line 1, in <module>
    from Numeric import *
    ImportError: No module named 'Numeric'
    >>> from Bio.Seq import Seq
    >>> from Bio.Alphabet.IUPAC import unambiguous_dna
    >>> new_seq = Seq('GATCAGAAG', unambiguous_dna)
    >>> new_seq[0:2]
    Seq('GA', IUPACUnambiguousDNA())
    >>> from Bio import Translate
    Traceback (most recent call last):
    File "<pyshell#7>", line 1, in <module>
    from Bio import Translate
    ImportError: cannot import name Translate
    >>>

  • #2
    Funnily enough, you installed Biopython correctly but your attempts to test your installation are incorrect.

    import Bio
    >>> print(Bio._version_)

    You must put double underscores instead of single underscores.
    Demonstration.

    >>> import Bio
    >>> print(Bio._version_)
    Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    AttributeError: 'module' object has no attribute '_version_'
    >>> print(Bio.__version__)
    1.64
    >>>

    ####

    The 2 other modules you are trying to use are deprecated.

    Module Numeric
    "There is a module called Numeric, but it's been deprecated for years in favour of numpy. You probably want to update your code to use numpy instead."
    I get the following error ImportError: No module named numeric if I have the following import from numeric import * in my python source code. How do I get this running on my Windows box agains...


    Module Translate
    "This module is now deprecated, and will be removed in a future release of Biopython."

    Comment


    • #3
      Hey, thank you !

      Comment


      • #4
        Hi anushavarma, thanks for the feedback. Perhaps there is some out of date documentation which we've overlooked - what were you reading which suggested testing a Biopython install with these commands in Python?

        Code:
        from Numeric import *
        from Bio import Translate
        The double underscore for checking the version can be hard to read so I've tried to clarify that for the next Biopython release:
        Official git repository for Biopython (originally converted from CVS) - Clarify the Bio.__version__ FAQ entry · biopython/biopython@e1885a1

        Comment

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