Skip to content

Creating gene annotation from GFF file fails  #1135

Open
@aminakur

Description

I am trying to create gene annotations file from GFF following this protocol:
https://github.com/higlass/gene_annotations
Receive an error:

Processing line #: 0
Traceback (most recent call last):
  File "scripts/gff_to_jsonl.py", line 116, in <module>
    main()
  File "scripts/gff_to_jsonl.py", line 84, in main
    for p in parts["attributes"].strip(";").split(";")
KeyError: 'attributes'

Could you please help me with this?

In addition, I cannot find file requirements.txt in the gene_annotations repository. Am I to use requirements.txt file from a different higlass repo?

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