Virusinterpreter Object

Virusinterpreter file parsing and manipulation.

Super class

nemo::Tool -> Virusinterpreter

Methods

Public methods

• Virusinterpreter$new()

• Virusinterpreter$parse_annotated()

• Virusinterpreter$tidy_annotated()

• Virusinterpreter$clone()

Inherited methods

• nemo::Tool$.eval_func()
• nemo::Tool$.parse_file()
• nemo::Tool$.parse_file_nohead()
• nemo::Tool$.tidy_file()
• nemo::Tool$filter_files()
• nemo::Tool$list_files()
• nemo::Tool$nemofy()
• nemo::Tool$print()
• nemo::Tool$tidy()
• nemo::Tool$write()

---

Method new()

Create a new Virusinterpreter object.

Usage

Virusinterpreter$new(
  path = NULL,
  files_tbl = NULL,
  tidy = TRUE,
  keep_raw = FALSE
)

Arguments

path

(character(1))
Output directory of tool. If files_tbl is supplied, this basically gets ignored.

files_tbl

(tibble(n))
Tibble of files from nemo::list_files_dir().

tidy

(logical(1))
Should the raw parsed tibbles get tidied?

keep_raw

(logical(1))
Should the raw parsed tibbles be kept in the final output?

---

Method parse_annotated()

Read virus.annotated.tsv file.

Usage

Virusinterpreter$parse_annotated(x)

Arguments

x

(character(1))
Path to file.

---

Method tidy_annotated()

Tidy virus.annotated.tsv file.

Usage

Virusinterpreter$tidy_annotated(x)

Arguments

x

(character(1))
Path to file.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Virusinterpreter$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cls <- Virusinterpreter
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "virusinterpreter_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "virusinterpreter.*parquet", full.names = FALSE))
#> character(0)