If you are at the IMP or IMBA then just log in with your username/password, no registration needed. GMI and MFPL members please use firstname.lastname as your username, and your professional e-mail address when registering.

Welcome to the BioComp Knowledge Hub! You can ask questions here related to bioinformatics, statistics, computational biology and similar subjects. You can also answer questions and rate other users' contributions.

Frequently Asked Questions

matplotlib import error

0 votes
1 view

Hey,
I installed the metaseq python package (https://pythonhosted.org/metaseq/index.html) and its dependencies on my mac via pip. However I have the problem using the libary as it produces the following error uppon importing. 

ImportError Traceback (most recent call last)

<ipython-input-7-e8cb22a5226b> in <module>()
----> 1 import metaseq
      2 import os
      3 import gffutils
      4 import multiprocessing
      5 import pybedtools

/Library/Python/2.7/site-packages/metaseq/__init__.py in <module>()
      9 import integration.chipseq
     10 import colormap_adjust
---> 11 import results_table
     12 import tableprinter
     13 from version import __version__

/Library/Python/2.7/site-packages/metaseq/results_table.py in <module>()
      9 import plotutils
     10 from matplotlib.transforms import blended_transform_factory
---> 11 from matplotlib.collections import EventCollection
     12 import gffutils
     13 import pybedtools

importing matplotlib.collections works fine, but I cant run from matplotlib.collections import EventCollection as it cannot be imported. However if i look in the collections.py file in the matplotlib folder I find that it contains a class called EventCollection.
Does anybody have suggestions on how to fix this problem?
Best wishes,

Falko

asked Jun 18, 2015 in Software development by falko.hofmann (400 points)

1 Answer

0 votes
 
Best answer
Ok, the issue was my virtual enviroments got messed up.
answered Sep 22, 2016 by falko.hofmann (400 points)
...