Copy LSV text below: empty when use voila view.

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Apr 18, 2021, 10:38:47 PMApr 18
to majiq_voila
Dear Paul,

I am using voila view, however, no .josn text was generated when I click the 'copy lsv' button. I would like to design RT-PCR primers by MAJIQ-SPEL.

I used the ucsc hg38 genome files which is download in ucsc.
gff file is converted from the gtf file.

command I used:
voila view /home/l/GI_DLBC/exrnaseq/results/majiq/build/splicegraph.sql /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/

2021-04-19 10:29:10,214 (PID:113567) - INFO - Command: /home/l/miniconda3/envs/MAJIQ/bin/voila view /home/l/GI_DLBC/exrnaseq/results/majiq/build/splicegraph.sql /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/
2021-04-19 10:29:10,215 (PID:113567) - INFO - Voila v2.0.0-05c9c32
2021-04-19 10:29:10,215 (PID:113567) - INFO - config file: /tmp/tmp1wqjjksy
2021-04-19 10:29:10,224 (PID:113567) - INFO - Using index: /home/l/GI_DLBC/exrnaseq/results/majiq/deltapsi/DLBC_NORMAL.deltapsi.voila
/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/ H5pyDeprecationWarning: dataset.value $
as been deprecated. Use dataset[()] instead.
  for row in h['index'].value: on /copy-lsv/ENSG00000001167:s:41079029-41079164 [POST]
Traceback (most recent call last):
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 2292, in wsgi_app
    response = self.full_dispatch_request()
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 1815, in full_dispatch_request
    rv = self.handle_user_exception(e)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 1718, in handle_user_exception
    reraise(exc_type, exc_value, tb)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 35, in reraise
    raise value
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 1813, in full_dispatch_request
    rv = self.dispatch_request()
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/flask/", line 1799, in dispatch_request
    return self.view_functions[rule.endpoint](**req.view_args)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/view/", line 287, in copy_lsv
    return views.copy_lsv(lsv_id, ViewDeltaPsi)
  File "/home/l/miniconda3/envs/MAJIQ/lib/python3.6/site-packages/voila/view/", line 92, in copy_lsv
    with ViewSpliceGraph() as sg, view_matrix(voila_file=voila_file) as m:
TypeError: __init__() got an unexpected keyword argument 'voila_file'


Paul Jewell

Apr 27, 2021, 5:00:05 PMApr 27
to majiq_voila
Hello Li, 

I believe this was a known older bug in Voila, and the issue was patched out in newer versions. Would you be able to install the newest version from the downloads page, and try again?


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