Open jqbeh opened 1 year ago
Hi mate. It would require writing a parser for these files. This could be done, but I am unfamiliar with this file type, could you provide some examples or some links to exampels?
Hi, thanks for the reply!
I am unable to upload the file here but you can download a sample GFF3 file from this link: https://www.ncbi.nlm.nih.gov/nuccore/NZ_LC495616.1
Since GFF3 files are already parsed in a tabular format, this is just a data wrangling problem to make it work with plot_plasmid(). For example, you can do:
library(tidyverse)
library(plasmapR)
dat <- read_tsv("sequence.gff3", comment = "#", col_names = FALSE) %>%
select(type = 3, start = 4, end = 5, direction = 7, attribute = 9) %>%
filter(!type %in% "gene") %>%
mutate(direction = ifelse(direction == "+", 1, -1),
type = ifelse(type == "region", "source", type),
name = ifelse(type == "source",
str_match(attribute, "Name=(\\w+);")[,2],
str_match(attribute, "locus_tag=(\\w+);")[,2])) %>%
rownames_to_column("index")
plot_plasmid(dat, dat$name[1])
Hi, thanks for making this wonderful package!
I was wondering if I could use .gff or .gff3 as input instead of .gb?
Thanks!