search

dieterich-lab / rp-bp

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.
MIT License
7 stars 5 forks source link

Extract-ORF-Coordinates Error #157

Closed bshim181 closed 10 months ago

bshim181 commented 10 months ago

Hello,

I am receiving a Extract-ORF-Coordinates error

Screenshot 2023-09-02 at 9 14 05 PM

stating key error 'seqname' I am using primary assembly (Grch37) from gencode with the same version gtf files. is there a reason why this error throws during orf coordinate labelling?

rpbp_genome.annotated.bed file seems to have #seqname as columns. I was wondering if this might be the issue?

Screenshot 2023-09-05 at 11 11 33 AM
eboileau commented 10 months ago

When you create an issue (Bug report -> Get started), there is a bug report template. You should fill it, and not delete it! I don't have enough information to help you, I don't know which version you use, which command you used (did you try DEBUG mode?), the stack trace is incomplete, I don't have access to your data (no idea if this bug is reproducible), etc.

I cannot reproduce this error. All tests passed. I also have re-installed the package in a fresh environment conda create -n rpbp rpbp, and created the genome indices and annotations prepare-rpbp-genome c-elegans-test.yaml --star-options "--genomeSAindexNbases 10" --num-cpus 4 --logging-level INFO --log-file rpbp-genome.log, as explained here https://rp-bp.readthedocs.io/en/latest/tutorial-cel.html, all without error.

I suggest that you first try to run the examples, see https://rp-bp.readthedocs.io/en/latest/tutorial.html, or run the tests, and if you can reproduce the bug, then open a new issue, with all relevant details. Thanks.