Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Creating gene annotation from GFF file fails #1135

Open
MyBiscuit opened this issue Nov 29, 2022 · 1 comment
Open

Creating gene annotation from GFF file fails #1135

MyBiscuit opened this issue Nov 29, 2022 · 1 comment

Comments

@MyBiscuit
Copy link

MyBiscuit commented Nov 29, 2022

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?

@pkerpedjiev
Copy link
Member

Sorry for the delayed response. Would you mind sending the input file and command you used?

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

No branches or pull requests

2 participants