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ding-lab / CharGer

Characterization of Germline variants
https://ding-lab.github.io/CharGer/
GNU General Public License v3.0
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errors #2

Closed luwening closed 6 years ago

luwening commented 6 years ago

python test_chargervariant.py

E

======================================================================

ERROR: test_nonzero (main.testchargervariant)

Traceback (most recent call last):

File "test_chargervariant.py", line 13, in test_nonzero

if ( v ):

File "/xxx/python2.7/site-packages/charger/chargervariant.py", line 201, in nonzero

elif ( self.checkIfRefAltStrand( k ) ):

AttributeError: 'chargervariant' object has no attribute 'checkIfRefAltStrand'

Ran 1 test in 0.001s

FAILED (errors=1)

amilacsw commented 6 years ago

Hi @luwening, Thanks for informing us about the error. This error is due to usage of outdated package in dependencies, Biomine. We updated the Biomine in Pypi to the most recent one (v0.9.5), which should fix the error you're encountering.

Please update CharGer using, pip install -U charger

or pull the latest version of charger and reinstall it using, cd path/to/CharGer git pull pip install .

Best, Amila