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chapmanb / bcbb

Incubator for useful bioinformatics code, primarily in Python and R
http://bcbio.wordpress.com
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GFFParser on python 3.3.2 #76

Closed ychenbioinfo closed 10 years ago

ychenbioinfo commented 10 years ago

Hi,

I tried to use GFFParser on python 3.3.2, but I got an error.

Python 3.3.2 (default, May 21 2013, 11:50:47) [GCC 4.2.1 Compatible Apple Clang 4.1 ((tags/Apple/clang-421.11.66))] on darwin Type "help", "copyright", "credits" or "license" for more information.

from BCBio import GFF Traceback (most recent call last): File "", line 1, in File "/opt/local/Library/Frameworks/Python.framework/Versions/3.3/lib/python3.3/site-packages/BCBio/GFF/init.py", line 3, in from GFFParser import GFFParser, DiscoGFFParser, GFFExaminer, parse, parse_simple ImportError: No module named 'GFFParser'

I installed it using pip "/Users/Alvin/Library/Python/3.3/bin/pip install bcbio-gff".

I am new to python, so I am not sure whether is it caused by improper installation or the different version of python.

Thanks, Alvin

chapmanb commented 10 years ago

Alvin; Unfortunately this module isn't compatible with Python 3. If you use version 2.7 using the same pip install approach it should work cleanly. Hope this fixes it for you.