Fixed kipoisplice

[haimasree]

I had to downgrade python version to 3.5 since pyvcf does not seem to be getting compiled with pyvcf

[Hoeze]

I cannot see where pyvcf is being imported. I think you can just remove this dependency. cyvcf2 is the better alternative :)

[haimasree]

Tried that before :). KipoiSplice uses kipoi-veff which needs pyvcf. Otherwise we will get the following error

Traceback (most recent call last):
  File "/opt/conda/envs/kipoi-KipoiSplice/bin/kipoi", line 8, in <module>
    sys.exit(main())
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi/__main__.py", line 105, in main
    command_fn(args.command, sys.argv[2:])
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi/cli/main.py", line 76, in cli_test
    mh.pipeline.predict_example(batch_size=args.batch_size, output_file=args.output, **{'keep_metadata': args.keep_metadata})
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi/pipeline.py", line 124, in predict_example
    dl = self.dataloader_cls.init_example()
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi/data.py", line 141, in init_example
    return cls(**cls.example_kwargs)
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi/data.py", line 280, in __init__
    self.data = self._get_data_fn()(*args, **kwargs)
  File "dataloader.py", line 124, in load_data
    scores=sel_scores)
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi_veff/snv_predict.py", line 775, in score_variants
    output_writers.append(VcfWriter(model, in_vcf_path_abs, out_vcf_path_abs, standardise_var_id=std_var_id))
  File "/opt/conda/envs/kipoi-KipoiSplice/lib/python3.6/site-packages/kipoi_veff/utils/io.py", line 259, in __init__
    import vcf
ModuleNotFoundError: No module named 'vcf'

[Hoeze]

hm what a pity :sweat_smile: