alimanfoo/pysamstats

error of pysamstats while using python2.7.14

Opened this issue · 5 comments

douym commented

Hi alimanfoo,

when I try to import pysamstats under python2, there is an error:

import pysamstats
Traceback (most recent call last):
File "", line 1, in
File "/n/data1/hms/dbmi/park/yanmei/tools/anaconda3/envs/python2/lib/python2.7/site-packages/pysamstats/init.py", line 8, in
from .pileup import *
File "/n/data1/hms/dbmi/park/yanmei/tools/anaconda3/envs/python2/lib/python2.7/site-packages/pysamstats/pileup.py", line 6, in
import pysamstats.opt as opt
File "libcfaidx.pxd", line 52, in init pysamstats.opt
AttributeError: 'module' object has no attribute 'FastxRecord'

if I import pysamstats under python3.6.1, then it's completely normal.

Do you know how should I do to fix that? thanks a lot!

alimanfoo commented

Hi @douym, this type of error is usually due to a version mismatch between pysamstats and pysam. The current release version of pysamstats (1.0.1) needs to be installed together with pysam version 0.11.2.2. E.g.:

pip install pysam==0.11.2.2
pip install pysamstats==1.0.1

You can check what versions you have installed, e.g.:

python -c 'import pysam; import pysamstats; print(pysam.__version__, pysamstats.__version__)'

I'm guessing your python2 environment has a different version of pysam.

alimanfoo commented

Closing but feel free to re-open if problem is not resolved.

frabanal commented

I have exactly the same error message when installing with conda. I've uninstalled both pysam and pysamstats, installed the correct versions (pysam==0.11.2.2 & pysamstats==1.0.1; btw, Python 2.7.14 :: Anaconda, Inc.), and the error persists. Do you have any extra ideas, please?

Unfortunately, at the moment, I can't install via pip, cause I've made the mistake of upgrading it, and I lost pip –working on solving this issue as well...

Thanks in advance for your support, I just wanna go back to work with pysamstats: such a useful tool!

alimanfoo commented

Apologies @frabanal this got lost in my email backlog. Did you solve this problem, or is it still relevant?

Lidweixiang commented

Hi alimanfoo,
I get the same error and my installation method as follow:
1.copy source code from github
2./pysamstats-master $ python setup.py install
[pysamstats] build with Cython
3.test:/pysamstats-master $ nosetests -v
Failure: ModuleNotFoundError (No module named 'pysamstats.opt') ... ERROR

======================================================================
ERROR: Failure: ModuleNotFoundError (No module named 'pysamstats.opt')
Something I have missed about the question?
hope your answer,thank you !