[BUG] Stop codons appear when anvi-inspect magnification truncates and ORF

[mschecht]

Short description of the problem

When users zoom into a region of genomic context that does not include the actual stop codon of an ORF, anvi-inspect will put a STP codon at the farthest downstream codon of the ORF.

anvi'o version

$ anvi-self-test --version

Anvi'o .......................................: marie (v8-dev)
Python .......................................: 3.10.13

Profile database .............................: 40
Contigs database .............................: 23
Pan database .................................: 17
Genome data storage ..........................: 7
Auxiliary data storage .......................: 2
Structure database ...........................: 2
Metabolic modules database ...................: 4
tRNA-seq database ............................: 2

System info

macOS 13.2.1 (22D68)

Detailed description of the issue

Here is a picture where I zoomed into an ORF and the STP codon appears. This is not the stop codon but just the last codon appearing in the zoomed in frame.

The actual STP codon is downstream:

Files / commands to reproduce the issue

cd INFANT-GUT-TUTORIAL

anvi-interactive

inspect a contig with ORFs and zoom in to show ORF plus non coding region that does not include the actual stop codon.

[metehaansever]

Hey @mschecht I've solved that bug couple of weeks ago. Did you update your branch from master?

This is how it looks like on my side:

[mschecht]

Hi @metehaansever, thanks for looking into this! I'm definitely on the main branch and can replicate the behavior in multiple contigs and contexts.

How should we move forward?

[metehaansever]

Okay this is new! Only the position of the STP codon behaves weird. I'll look into it. :+1: