problems installing HTSeq

Question

[Lila M]

Hi everybody

I'm analyzing some data using DEXSEq, for that proposal I've used

python2.7 home/my_user/R/x86_64-pc-linux-gnu-library/3.3/DEXSeq/python_scripts/dexseq_prepare_annotation.py Homo_sapiens.GRCh37.75.gtf Homo_sapiens.GRC37.gff3

And I get the next error mesage

Could not import HTSeq. Please install the HTSeq Python framework
available from http://www-huber.embl.de/users/anders/HTSeq

However, I have HTSeq installed, but when I open python2 and type

>>> import HTSeq

I get :

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/my_user/.local/lib/python2.7/site-packages/HTSeq-0.7.2-py2.7-linux-x86_64.egg/HTSeq/__init__.py", line 9, in <module>
    from _HTSeq import *
  File "python2/src/HTSeq/_HTSeq.pyx", line 14, in init HTSeq._HTSeq (src/_HTSeq.c:39182)
  File "/home/my_user/.local/lib/python2.7/site-packages/HTSeq-0.7.2-py2.7-linux-x86_64.egg/HTSeq/StepVector.py", line 17, in <module>
    _StepVector = swig_import_helper()
  File "/home/my_user/.local/lib/python2.7/site-packages/HTSeq-0.7.2-py2.7-linux-x86_64.egg/HTSeq/StepVector.py", line 16, in swig_import_helper
    return importlib.import_module('_StepVector')
  File "/home/my_user/miniconda3/envs/py27/lib/python2.7/importlib/__init__.py", line 37, in import_module
    __import__(name)
ImportError: No module named _StepVector

Any clues about what is going on or what I should do?

Thanks!

Answer 1

[Devon Ryan]

It looks a lot like you're mixing and matching between conda and pip, which can lead to a LOT of headaches. Try the following:

• rm -rf /home/my_user/.local/lib/python2.7/site-packages/HTSeq*
• conda install -c bioconda htseq

This may fix your issue.

[Lila M]

As always Davon, problem solved :)

Thank you so much!