Clinical-Genomics / fusion-report

Tool for parsing outputs from fusion detection tools. Part of a nf-core/rnafusion pipeline. Checkout a live demo at https://matq007.github.io/fusion-report/example/

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Access dictionary using get with default

matq007 opened this issue · comments

  Traceback (most recent call last):
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/bin/fusion_report", line 13, in <module>
      app.run()
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/lib/python3.7/site-packages/fusion_report/app.py", line 60, in run
      self.preprocess(params)
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/lib/python3.7/site-packages/fusion_report/app.py", line 82, in preprocess
      self.enrich(params.db_path)
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/lib/python3.7/site-packages/fusion_report/app.py", line 141, in enrich
      MitelmanDB(path).name: MitelmanDB(path).get_all_fusions(),
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/lib/python3.7/site-packages/fusion_report/data/mitelman.py", line 20, in get_all_fusions
      return [fusion['geneshort'].strip().replace('/', '--') for fusion in res]
    File "/opt/conda/envs/nf-core-rnafusion-1.2.0/lib/python3.7/site-packages/fusion_report/data/mitelman.py", line 20, in <listcomp>
      return [fusion['geneshort'].strip().replace('/', '--') for fusion in res]
  KeyError: 'geneshort'