JCVI codon table generation is flat-out-wrong

[Koeng101]

It returns:

* has the following weights:
[  "TAA: 4680",  "TAG: 1369"]

This is impossible, as JCVI has <500 genes.

[TimothyStiles]

Are you passing the whole sequence or just the CDS sequences?

On Sat, May 6, 2023, 11:21 PM Koeng101 @.***> wrote:

It returns:

• has the following weights: [ "TAA: 4680", "TAG: 1369"]

This is impossible, as JCVI has <500 genes.

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[Koeng101]

Turns out, some genes were noted to be pseudo genes, but still had feature type of CDS. This caused the entire thing to fail. I think docs should be updated with this. Adding another pr.

for _, feature := range sequence.Features {
        if feature.Type == "CDS" {
            if _, ok := feature.Attributes["pseudo"]; ok {
                continue
            }
            seq, _ := feature.GetSequence()
            codingRegionsBuilder.WriteString(seq)
            genes++
        }
    }