A user reported this issue as part of issue #227, spinning it off into it's own thing.
When trying to create a cohort object with mhcnames v 1.2.0 in python 3.6, he encountered the following error:
ImportError: cannot import name 'AlleleParseError'
He reported using mhcnames vs 1.2.0 & mhctools v 1.5.0.
I put together the following test case in an attempt to reproduce the error, which I then tested as I upgraded first mhcnames to v 1.2.0 & then mhctools to v 1.5.0.
The following worked fine with mhcnames v 1.20 & mhctools v 1.3.0, but 'broke' when I updated mhctools to 1.5.0.
The traceback when using mhctools 1.5.0 is included here:
(rcc) jacquelineburos@jacki2:~/projects/cohorts2/test$ python
Python 3.5.2 |Continuum Analytics, Inc.| (default, Jul 2 2016, 17:53:06)
[GCC 4.4.7 20120313 (Red Hat 4.4.7-1)] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> from cohorts import Patient, Cohort
Using TensorFlow backend.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jacquelineburos/projects/cohorts/cohorts/__init__.py", line 15, in <module>
from .cohort import Cohort
File "/home/jacquelineburos/projects/cohorts/cohorts/cohort.py", line 42, in <module>
from mhctools import NetMHCcons, EpitopeCollection
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/__init__.py", line 12, in <module>
from .netmhc import NetMHC
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/netmhc.py", line 20, in <module>
from .netmhc3 import NetMHC3
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/netmhc3.py", line 17, in <module>
from .base_commandline_predictor import BaseCommandlinePredictor
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/base_commandline_predictor.py", line 24, in <module>
from mhcnames.parsing_helpers import AlleleParseError
ImportError: cannot import name 'AlleleParseError'
>>> from cohorts.functions import neoantigen_count
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/jacquelineburos/projects/cohorts/cohorts/__init__.py", line 15, in <module>
from .cohort import Cohort
File "/home/jacquelineburos/projects/cohorts/cohorts/cohort.py", line 42, in <module>
from mhctools import NetMHCcons, EpitopeCollection
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/__init__.py", line 12, in <module>
from .netmhc import NetMHC
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/netmhc.py", line 20, in <module>
from .netmhc3 import NetMHC3
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/netmhc3.py", line 17, in <module>
from .base_commandline_predictor import BaseCommandlinePredictor
File "/home/jacquelineburos/miniconda3/envs/rcc/lib/python3.5/site-packages/mhctools/base_commandline_predictor.py", line 24, in <module>
from mhcnames.parsing_helpers import AlleleParseError
ImportError: cannot import name 'AlleleParseError'
Which, in fact, doesn't require any test data since the error is on
A user reported this issue as part of issue #227, spinning it off into it's own thing.
When trying to create a cohort object with mhcnames v 1.2.0 in python 3.6, he encountered the following error:
He reported using mhcnames vs 1.2.0 & mhctools v 1.5.0.
I put together the following test case in an attempt to reproduce the error, which I then tested as I upgraded first mhcnames to v 1.2.0 & then mhctools to v 1.5.0.
The following worked fine with mhcnames v 1.20 & mhctools v 1.3.0, but 'broke' when I updated mhctools to 1.5.0.
The traceback when using mhctools 1.5.0 is included here:
Which, in fact, doesn't require any test data since the error is on