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XiaoTaoWang / EagleC

A deep-learning framework for predicting a full range of structural variations from bulk and single-cell contact maps
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How to give reference genome version when running gene fusion #44

Open Krithika-Bhuvan opened 2 months ago

Krithika-Bhuvan commented 2 months ago

Hello, I am attempting to run the gene fusion anotation on the output of my Eaglec SVs (code below). The documentation example offers --ensembl-release setting which only specifies the version of ensembl db to use. By default Grch38 is being used with db version 93. I would like to use hg19 or Grch37. I'm not seeing any optional argument for genome version. Can you explain how i can do this ?

annotate-gene-fusion --sv-file $SVFILE \
                       --output-file $OUTFILE \
                       --buff-size 10000 \
                       --skip-rows 1 \
                       --ensembl-release 93 \
                       --species human

Also got this error when running genefusion with the above settings i mentioned. Can you please see why this happened ?

  File "/usr/local/apps/eaglec/conda/envs/0.1.9/lib/python3.8/site-packages/datacache/database_types.py", line 96, in db_type
    raise ValueError("Failed to find sqlite3 column type for %s" % (
ValueError: Failed to find sqlite3 column type for category