Unable to install biopython on windows properly

[anushavarma]

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
>>>

[blancha]

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."

http://stackoverflow.com/questions/8210344/importerror-no-module-named-numeric

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

http://biopython.org/DIST/docs/_api_158/Bio.Translate-module.html

[anushavarma]

Hey, thank you !

[maubp]

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 Perhaps there is some out of date documentation which we've overlooked - what were you reading which suggested testing a Biopython install with these commands in Python?

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:

https://github.com/biopython/biopython/commit/e1885a12ede1297a59c11206da41749d4a7d2b76