feature names hardcoded in extract_annotations_from_gff.py

[mohammedkhalfan]

Description of the bug

I'm not sure if this is a bug or by design. There are parameters to override the default feature names in the host and pathogen annotations, but I'm not sure if they are being used in all parts of the pipeline. For instance, I get failures when running the step which calls extract_annotations_from_gff.py because it cannot find any features. When I look in the script I can see that 'gene_type', 'gene_id', 'gene_name', and 'transcript_name' are hardcoded, and thus the parameters which I specify to override these feature names are not used in this script. If I manually edit this file to use the corresponding feature names, it works.

Steps to reproduce

Use a reference annotation from Ensembl such as Saccharomyces_cerevisiae.R64-1-1.34.gff3 or Schizosaccharomyces_pombe.ASM294v2.51.gff3 which does not contain the default feature names.

Expected behaviour

I expect the feature names I specify when running the pipeline to override the default names, but the names in this script are hardcoded.

[reganhayward]

Hi @mohammedkhalfan,
Thanks for you precise report!
Looks like you are right, this does need to be updated. I'll tag @bozmik as she should be able to update this easily.
We're currently working behind the scenes updating the pipeline, which will include the template updates as well.
I'll keep this bug open until we have a new release - just so others are aware
Thanks again for reporting this
Regan