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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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CSQ field is not parsed properly in genmod score when using --skip_plugin_check #85

Open hassanfa opened 6 years ago

hassanfa commented 6 years ago

Genmod version: 3.7.0 (replicated in 3.7.2 as well)

command: genmod score -s --skip_plugin_check -f sample.ped -c rank_model.ini -t ped new_sample.vcf

I am using a custom made rank model with CSQ field from the template. I get the following error while trying to run it on my VCF file from VEP's output. The error occurs only when I have the CSQ field in my ranked model. When I expand it into other info fields, it doesn't happen. So I suppose it is a CSQ field issue only.

Traceback (most recent call last):
  File "/Users/hassanforoughi/miniconda3/envs/scout/bin/genmod", line 11, in <module>
    sys.exit(cli())
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/core.py", line 722, in __call__
    return self.main(*args, **kwargs)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/core.py", line 697, in main
    rv = self.invoke(ctx)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/core.py", line 895, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/core.py", line 535, in invoke
    return callback(*args, **kwargs)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/click/decorators.py", line 17, in new_func
    return f(get_current_context(), *args, **kwargs)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/genmod/commands/score_variants.py", line 177, in score
    csq_format=csq_format
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/genmod/score_variants/score_variant.py", line 59, in get_category_score
    csq_format = csq_format
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/genmod/score_variants/score_variant.py", line 27, in get_plugin_score
    value = plugin.get_value(variant_dict=variant, csq_format=csq_format)
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/extract_vcf/plugin.py", line 354, in get_value
    individual_id=individual_id):
  File "/Users/hassanforoughi/miniconda3/envs/scout/lib/python3.6/site-packages/extract_vcf/plugin.py", line 136, in get_entry
    entry += split_strings(csq_entry.split('|')[csq_column], self.separators)
UnboundLocalError: local variable 'csq_column' referenced before assignment

The VCF file has a standard VCF format and it is VEP's raw output.