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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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NameError: global name 'entrezaip' is not defined when doing clinvar search #52

Open mingoo426 opened 3 years ago

mingoo426 commented 3 years ago

Hi CharGer Team!

whenever I try to use clinvar using the -l option, I encounter this error:

charger::getClinVar
warning: ClinVar ReST search batch size given is greater than max allowed (50). Overriding to max search batch size.
Traceback (most recent call last):
  File "/home/minku/anaconda3/envs/charger/bin/charger", line 744, in <module>
    main( sys.argv[1:] )
  File "/home/minku/anaconda3/envs/charger/bin/charger", line 663, in main
    mutationTypes = mutationTypes , \
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 879, in getExternalData
    self.getClinVar( **kwargs )
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 905, in getClinVar
    self.getClinVarviaREST( **kwargs )
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/charger/charger.py", line 918, in getClinVarviaREST
    ent = entrezapi()
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/biomine/webapi/entrez/entrezapi.py", line 74, in __init__
    self.setRequestLimits()
  File "/home/minku/anaconda3/envs/charger/lib/python2.7/site-packages/biomine/webapi/entrez/entrezapi.py", line 332, in setRequestLimits
    self.setSummaryBatchSize( entrezaip.summaryBatchSize )
NameError: global name 'entrezaip' is not defined

Is entrezaip supposed to be entrezapi on line 332 and 333?

Thank you! :)