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I'm trying to import a QIIME script as a module. The script works when I call it through linux cmd, but when I import the QIIME script as a module, I get the error 

~/VirtualENV/lib/python2.7/site-packages/skbio/alignment/_ssw_wrapper.so:undefined symbol: PyUnicodeUCS2_Format

It seems to have a problem with the following line from skbio:

from skbio.alignment._ssw_wrapper import (
    StripedSmithWaterman, local_pairwise_align_ssw, AlignmentStructure)

My IDE is Spyder. After the first time I got the error, I changed my console (in the tools menu) to the same python interpreter as my VirtualENV containing the QIIME packages. I'm running python 2.7. My VirtualENV is in my pythonpath. Is there something I can add to my path to fix this? Thanks in advance, I'm new to importing scripts.

Tichigan
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  • What version of scikit-bio do you have installed? scikit-bio 0.5.0 and later only support Python 3.4 and later. What platform do you have it installed on (e.g. Linux, Mac, Windows)? For your QIIME 1 questions I recommend posting to the [QIIME 1 forum](http://forum.qiime.org). – jairideout Feb 24 '17 at 15:48
  • According to __init__.py, I'm using 0.2.3. I am running it on Linux in a VirtualENV. – Tichigan Feb 24 '17 at 21:33
  • Can you post an issue on the scikit-bio issue tracker? That'll be more efficient than troubleshooting your installation problems via Stackoverflow comments. Please include the commands you ran to install scikit-bio. Thanks! https://github.com/biocore/scikit-bio/issues – jairideout Feb 27 '17 at 16:49
  • Ok, I'll move over there. Not an installation problem, though. – Tichigan Mar 02 '17 at 00:36
  • Thanks! I suspect it is an installation problem related to your platform because the SSW code can't be imported. I see that scikit-bio is "installed" on your system but you're not able to import anything from it, making it effectively unusable. – jairideout Mar 03 '17 at 17:27
  • Some other tools (e.g. biom) are giving unicode errors, and it seems like the problems are all stemming from .so files. I found [this](http://stackoverflow.com/questions/32078764/how-are-python-modules-which-are-shared-libraries-imported-without-a-py-file) and [this](http://stackoverflow.com/questions/9542357/how-do-so-files-work-and-where-do-they-go-in-unix). So, I'm trying to figure out where to go from there. – Tichigan Mar 03 '17 at 21:38
  • Yep, those .so files are the culprit, due to an issue with the SSW code on your system. We will continue helping you on [the issue](https://github.com/biocore/scikit-bio/issues/1502) you created on the issue tracker. Otherwise we will pollute your SO question with a bunch of comments -- it's going to require some back-and-forth to identify the issue, thus it's not the best place to work that out here. – jairideout Mar 06 '17 at 16:30

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