SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Unable to install Bioconductor packages with biocLite... gmpune Bioinformatics 9 01-27-2014 01:23 AM
Trinity will not install properly on Mac OS X godzilla07 Bioinformatics 4 11-07-2013 01:59 PM
Running Mac on Windows or Get Windows Laptop lsbrath General 23 04-04-2012 07:22 AM
unable to install 'pasilla' on R sridhar228 Bioinformatics 1 10-05-2011 10:30 PM
Install tabix on windows Scotch Bioinformatics 1 02-07-2011 12:19 AM

Reply
 
Thread Tools
Old 10-31-2014, 06:30 AM   #1
anushavarma
Junior Member
 
Location: Tampa

Join Date: Oct 2014
Posts: 4
Default 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
>>>
anushavarma is offline   Reply With Quote
Old 10-31-2014, 07:32 AM   #2
blancha
Senior Member
 
Location: Montreal

Join Date: May 2013
Posts: 367
Default

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/8...-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_...te-module.html
blancha is offline   Reply With Quote
Old 10-31-2014, 07:41 AM   #3
anushavarma
Junior Member
 
Location: Tampa

Join Date: Oct 2014
Posts: 4
Default

Hey, thank you !
anushavarma is offline   Reply With Quote
Old 11-01-2014, 04:19 AM   #4
maubp
Peter (Biopython etc)
 
Location: Dundee, Scotland, UK

Join Date: Jul 2009
Posts: 1,543
Default

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:
https://github.com/biopython/biopyth...41749d4a7d2b76
maubp is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO