non-informative error message

neksa / mutagene

Python library and package for mutational analysis

https://www.ncbi.nlm.nih.gov/projects/mutagene/

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non-informative error message #54

Closed anna-panchenko closed 3 years ago

anna-panchenko commented 3 years ago

Specifying the wrong genome assembly returns an error about the maf format: (env_mutagene) Annas-MacBook-Pro:mutagene panch$ mutagene -v rank -g hg18 -i TCGA.UCEC.mutect.somatic.maf WARNING Parsing MAF failed. Check that the input file is in MAF format or specify a different format using option -f FileNotFoundError(2, 'No such file or directory')

neksa commented 3 years ago

Confirmed. If hg18.2bit is not found the message is misleading.

shandy79 commented 3 years ago

I'll look into providing a more informative error message.

shandy79 commented 3 years ago

Closed w/PR 57