Skip to content

TypeError: 'NoneType' object is not subscriptable #82

@ywilke

Description

@ywilke

I am trying to run ANARCI on large number of sequences and I am getting the following error.
I cannot narrow it down to which sequence is causing the error.

  File "/local_disk0/.ephemeral_nfs/envs/pythonEnv-298aff8b-ef33-42af-99ab-0bfccbc42e7c/lib/python3.9/site-packages/anarci/anarci.py", line 941, in run_anarci
    csv_output(sequences, numbered, alignment_details, outfile)
  File "/local_disk0/.ephemeral_nfs/envs/pythonEnv-298aff8b-ef33-42af-99ab-0bfccbc42e7c/lib/python3.9/site-packages/anarci/anarci.py", line 287, in csv_output
    details[i][j].get('germlines',{}).get( 'j_gene',[['',''],0] )[0][1],
TypeError: 'NoneType' object is not subscriptable

It seems a None snuck into the j_gene value. The csv_output function can't handle a None.

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

    Milestone

    No milestone

    Relationships

    None yet

    Development

    No branches or pull requests

    Issue actions