In-frame indels shouldn't necessarily be "genes_inactivated"

[dannagifford]

When running gdtools COMPARE -f TSV, in frame deletions (here, Δ3 bp) are being recorded under the "genes_inactivated" column. I think "genes_inactivated" should only definitely apply to indels that generate a frameshift, i.e. mod(bp, 3)!=0

Maybe this was a deliberate choice--if so, it might be useful to mention in the docs somewhere.

The gene where I noticed this is an essential gene (gyrA), so I don't think it can be inactivated.

> MG1655_evo_muts %>% select(type, size, gene_name, genes_inactivated, genes_overlapping, genes_promoter) %>% filter(gene_name == "gyrA")

A tibble: 40 × 6
type size gene_name genes_inactivated genes_overlapping genes_promoter

1 SNP NA gyrA NA gyrA NA
2 DEL 3 gyrA gyrA NA NA
3 DEL 3 gyrA gyrA NA NA
4 DEL 3 gyrA gyrA NA NA
5 DEL 3 gyrA gyrA NA NA
6 DEL 3 gyrA gyrA NA NA
7 SNP NA gyrA NA gyrA NA
8 SNP NA gyrA NA gyrA NA
9 DEL 3 gyrA gyrA NA NA
10 DEL 3 gyrA gyrA NA NA

[jeffreybarrick]

Agree... looking into this logic.

[dannagifford]

I've also found that Δ1bp can also be called as "genes_overlapping" and sometimes "genes_inactivated" so I'm not really sure what overall is happening. Here, compare ompF and rapA. I've checked and the position of both mutations falls within the coding region. Both genes are on the reverse strand.

MG1655_mutations %>% filter(!is.na(size)) %>% select(type, size, position, gene_name, genes_inactivated, genes_overlapping, genes_promoter) %>% unique()