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bxlab / bx-python

Tools for manipulating biological data, particularly multiple sequence alignments
MIT License
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ImportError maf #11

Closed gfudenberg closed 3 years ago

gfudenberg commented 7 years ago

from bx.align import maf raises an ImportError undefined symbol: PyString_FromStringAndSize

On line 10 of seekbzip2.py from ._seekbzip2 import SeekBzip2

(in ipython3)

mkorycinski commented 7 years ago

Hi,

Is there a fix for that issue? I experience the same thing while using Python 3.5.2:

In [5]: import bx.align.maf
---------------------------------------------------------------------------
ImportError                               Traceback (most recent call last)
<ipython-input-5-21b2f5031b71> in <module>()
----> 1 import bx.align.maf

/usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/align/maf.py in <module>()
     12 from bx import interval_index_file
     13 from bx.align import *
---> 14 from bx.misc.seekbzip2 import SeekableBzip2File
     15 
     16 MAF_INVERSE_STATUS = 'V'

/usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/misc/seekbzip2.py in <module>()
      8 from six import Iterator
      9 
---> 10 from ._seekbzip2 import SeekBzip2
     11 
     12 

ImportError: /usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/misc/_seekbzip2.cpython-35m-x86_64-linux-gnu.so: undefined symbol: PyString_FromStringAndSize

Problem does not seem to appear in Python 2.7 though.

Thank you in advance for your help!

With best regards, Mateusz

jxtx commented 7 years ago

We currently do not support Python3 On Fri, Jun 2, 2017 at 7:36 AM Mateusz Korycinski notifications@github.com wrote:

Hi,

Is there a fix for that issue? I experience the same thing while using Python 3.5.2:

In [5]: import bx.align.maf---------------------------------------------------------------------------ImportError Traceback (most recent call last) in ()----> 1 import bx.align.maf /usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/align/maf.py in () 12 from bx import interval_index_file 13 from bx.align import *---> 14 from bx.misc.seekbzip2 import SeekableBzip2File 15 16 MAF_INVERSE_STATUS = 'V' /usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/misc/seekbzip2.py in () 8 from six import Iterator 9 ---> 10 from ._seekbzip2 import SeekBzip2 11 12 ImportError: /usr/local/lib/python3.5/dist-packages/bx_python-0.8.0-py3.5-linux-x86_64.egg/bx/misc/_seekbzip2.cpython-35m-x86_64-linux-gnu.so: undefined symbol: PyString_FromStringAndSize

Problem does not seem to appear in Python 2.7 though.

Thank you in advance for your help!

With best regards, Mateusz

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mkorycinski commented 7 years ago

Ok, I see. Thanks for fast reply!

nsoranzo commented 3 years ago

This is fixed, Python 3 has been supported for some time.