Example code missing files?

[cramsing]

I am trying to run through the example code you helpfully have prepared in your vignettes/emales.Rmd, but am running into some issues. I realize the code is dated and have mostly worked around this, but cannot get past the first visualization step.

# parse sequence length and some metadata from fasta file emale_seqs <- read_fai("emales.fna") %>% tidyr::extract(seq_desc, into = c("emale_type", "is_typespecies"), "=(\\S+) \\S+=(\\S+)", remove=F, convert=T) %>% dplyr::arrange(emale_type, length)

^This above chunk works with simply emale_seqs <- read_seqs("emales.fna") , but does not import any start or end data, likley because the "emales.fna" file does not have any.

This makes the visualization step impossible (see below) as there is no start or end information. Do you combine this file with another, ex. annotation/gff file?

# plot the genomes - first six only to keep it simple for this example emale_seqs_6 <- emale_seqs[1:6,] p1 <- [gggenomes](https://thackl.github.io/gggenomes/reference/gggenomes.html)(emale_seqs_6) + [geom_seq](https://thackl.github.io/gggenomes/reference/geom_seq.html)() + [geom_bin_label](https://thackl.github.io/gggenomes/reference/geom_bin_label.html)() p1

Thanks!

[thackl]

Hi Charis,

yeah, sorry for the outdated tutorial. Just to much on my plate to find the time and properly update it... You can use ex() to access gggenomes example data.

emale_seqs <- read_seqs(ex("emales/emales.fna"))