Kipoi-veff fails silently when the input files don't exist

kipoi / kipoi-veff

Variant effect prediction plugin for Kipoi

https://kipoi.org/veff-docs

MIT License

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Kipoi-veff fails silently when the input files don't exist #23

Closed Avsecz closed 5 years ago

Avsecz commented 6 years ago

The following command fails silently:

kipoi veff score_variants DeepBind/Homo_sapiens/TF/D00328.018_ChIP-seq_CTCF \
>    --dataloader_args='{"fasta_file": "input/hg19.chr22.fa"}' \
>    -i input/clinvar_20180429.chr22.pathogenic.vcf.gz \
>    -s ref alt diff \
>    -o /tmp/annotated.vcf

I executed it in the root of https://github.com/kipoi/examples where the file input/... doesn't exist.

krrome commented 5 years ago

I assume this a duplication of / at least related to: https://github.com/kipoi/kipoi/issues/314

krrome commented 5 years ago

copy of https://github.com/kipoi/kipoi-veff/issues/18