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kipoi / kipoi-veff

Variant effect prediction plugin for Kipoi
https://kipoi.org/veff-docs
MIT License
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dataloader_args #34

Closed ggabernet closed 5 years ago

ggabernet commented 5 years ago

Hi,

I am trying to test the kipoi-veff cli taking by example the command in the Kipoi paper, but I get an error:

Traceback (most recent call last):
  File "/Users/gisela/anaconda3/envs/kipoi-veff/bin/kipoi", line 10, in <module>
    sys.exit(main())
  File "/Users/gisela/anaconda3/envs/kipoi-veff/lib/python3.6/site-packages/kipoi/__main__.py", line 104, in main
    command_fn(args.command, sys.argv[2:])
  File "/Users/gisela/anaconda3/envs/kipoi-veff/lib/python3.6/site-packages/kipoi_veff/__main__.py", line 11, in cli_main
    kipoi_veff.cli.cli_main(command, raw_args)
  File "/Users/gisela/anaconda3/envs/kipoi-veff/lib/python3.6/site-packages/kipoi_veff/cli.py", line 458, in cli_main
    command_fn(args.command, raw_args[1:])
  File "/Users/gisela/anaconda3/envs/kipoi-veff/lib/python3.6/site-packages/kipoi_veff/cli.py", line 180, in cli_score_variants
    dataloader_arguments = parse_json_file_str_or_arglist(args.dataloader_args)
  File "/Users/gisela/anaconda3/envs/kipoi-veff/lib/python3.6/site-packages/kipoi_utils/utils.py", line 282, in parse_json_file_str_or_arglist
    raise RuntimeError("wrong usage, dataloader_args must be a list")
RuntimeError: wrong usage, dataloader_args must be a list

My command:

kipoi veff score_variants DeepSEA --dataloader_args '{"fasta_file": "~/.vep/homo_sapiens/97_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa"}' -i 'input.vcf' -o 'output.vcf'

I've also tested:

kipoi veff score_variants DeepSEA --dataloader_args='{"fasta_file": "~/.vep/homo_sapiens/97_GRCh37/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa"}' -i 'input.vcf' -o 'output.vcf'

to no avail.

ggabernet commented 5 years ago

turned out to be an old version of kipoi

Avsecz commented 5 years ago

Glad that fixed it:)