Minor bug/suggestion for genbank output

raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data

BSD 3-Clause "New" or "Revised" License

46 stars 7 forks source link

Minor bug/suggestion for genbank output #21

Closed pck00 closed 1 week ago

pck00 commented 2 months ago

Hello!

Loving the newest feature of getting genbank output files for the annotation.

One small issue: The LOCUS line is missing information on genome length and type (DNA, circular, linear). This causes errors with importing these files into Geneious and perhaps other genome viewers. It's easy to fix with a script but would be nice to have included right away in the output.

cheers

pck00 commented 2 months ago

Oh an a more major bug - the annotations in genbank format also do not come with directional information - so all the annotations face the same directions even if the actual coding sequences do not.

decrevi commented 2 months ago

Hello, Thank you for your feedback! We will make sure to include these fixes in the next update to MetaCerberus. I will post another comment here when it is ready.

-Jose

decrevi commented 1 week ago

Hello, MetaCerberus 1.4.0 is now live on Bioconda. Among other changes and improvements, I implemented some of your suggestions here. The GenBank output is still in development, and there are some things that MetaCerberus just cannot guess on so they are left blank. For now it is meant more as a template to make it easier to create a genbank file for importing into other software.

I did fix the directional information issue, please let me know if there are further issues or suggestions.

thank you, -Jose