Tool Object

Base class for all nemo tools.

Public fields

name

(character(1))
Name of tool.

path

(character(1))
Output directory of tool.

config

(Config())
Config of tool.

files

(tibble())
Tibble of files matching available Tool patterns.

tbls

(tibble())
Tibble of tidy tibbles.

raw_schemas_all

(tibble())
All raw schemas for tool.

tidy_schemas_all

(tibble())
All tidy schemas for tool.

get_tidy_schema

(function())
Get specific tidy schema.

get_raw_schema

(function())
Get specific raw schema.

files_tbl

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

Methods

Public methods

• Tool$new()

• Tool$print()

• Tool$filter_files()

• Tool$list_files()

• Tool$.parse_file()

• Tool$.tidy_file()

• Tool$.parse_file_keyvalue()

• Tool$.parse_file_nohead()

• Tool$.eval_func()

• Tool$tidy()

• Tool$write()

• Tool$nemofy()

• Tool$clone()

---

Method new()

Create a new Tool object.

Usage

Tool$new(name = NULL, pkg = NULL, path = NULL, files_tbl = NULL)

Arguments

name

(character(1))
Name of tool.

pkg

(character(1))
Package name tool belongs to (for config lookup).

path

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

files_tbl

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

---

Method print()

Print details about the Tool.

Usage

Tool$print(...)

Arguments

...

(ignored).

Returns

self invisibly.

---

Method filter_files()

Filter files in given tool directory.

Usage

Tool$filter_files(include = NULL, exclude = NULL)

Arguments

include

(character(n))
Files to include.

exclude

(character(n))
Files to exclude.

Returns

The tibble of files with potentially removed rows.

---

Method list_files()

List files in given tool directory.

Usage

Tool$list_files(type = "file")

Arguments

type

(character(1))
File type(s) to return (e.g. any, file, directory, symlink). See fs::dir_info.

Returns

A tibble of file paths.

---

Method .parse_file()

Parse file.

Usage

Tool$.parse_file(x, name, delim = "\t", ...)

Arguments

x

(character(1))
File path.

name

(character(1))
Parser name (e.g. "breakends" - see docs).

delim

(character(1))
File delimiter.

...

Passed on to readr::read_delim.

Returns

A tibble with the parsed data.

---

Method .tidy_file()

Tidy file.

Usage

Tool$.tidy_file(x, name, convert_types = FALSE)

Arguments

x

(character(1) or tibble())
File path or already parsed raw tibble.

name

(character(1))
Parser name (e.g. "breakends" - see docs).

convert_types

(logical(1))
Convert field types based on schema.

Returns

A tibble with the tidy data enframed.

---

Method .parse_file_keyvalue()

Parse files with no header and two columns representing key-value pairs.

Usage

Tool$.parse_file_keyvalue(x, name, delim = "\t", ...)

Arguments

x

(character(1))
File path.

name

(character(1))
Parser name (e.g. "qc" - see docs).

delim

(character(1))
File delimiter.

...

Passed on to readr::read_delim.

Returns

A tibble with the parsed data.

---

Method .parse_file_nohead()

Parse headless file.

Usage

Tool$.parse_file_nohead(x, pname, delim = "\t", ...)

Arguments

x

(character(1))
File path.

pname

(character(1))
Parser name (e.g. "breakends" - see docs).

delim

(character(1))
File delimiter.

...

Passed on to readr::read_delim.

Returns

A tibble with the parsed data.

---

Method .eval_func()

Evaluate function in the context of the Tool's environment.

Usage

Tool$.eval_func(fun, envir = self)

Arguments

fun

(character(1))
Function from Tool to evaluate.

envir

(environment())
Environment to evaluate the function within.

Returns

The evaluated function.

---

Method tidy()

Tidy a list of files.

Usage

Tool$tidy(tidy = TRUE, keep_raw = FALSE)

Arguments

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?

Returns

self invisibly.

---

Method write()

Write tidy tibbles.

Usage

Tool$write(
  diro = ".",
  format = "tsv",
  input_id = NULL,
  output_id = ulid::ulid(),
  dbconn = NULL
)

Arguments

diro

(character(1))
Directory path to output tidy files. Ignored if format is db.

format

(character(1))
Format of output.

input_id

(character(1))
Input ID to use for the dataset (e.g. run123).

output_id

(character(1))
Output ID to use for the dataset (e.g. run123).

dbconn

(DBIConnection)
Database connection object (see DBI::dbConnect).

Returns

A tibble with the tidy data and their output location prefix.

---

Method nemofy()

Parse, filter, tidy and write files.

Usage

Tool$nemofy(
  diro = ".",
  format = "tsv",
  input_id = NULL,
  output_id = ulid::ulid(),
  dbconn = NULL,
  include = NULL,
  exclude = NULL
)

Arguments

diro

(character(1))
Directory path to output tidy files.

format

(character(1))
Format of output.

input_id

(character(1))
Input ID to use for the dataset (e.g. run123).

output_id

(character(1))
Output ID to use for the dataset (e.g. run123).

dbconn

(DBIConnection)
Database connection object (see DBI::dbConnect).

include

(character(n))
Files to include.

exclude

(character(n))
Files to exclude.

Returns

A tibble with the tidy data and their output location prefix.

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Tool$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

if (FALSE) { # \dontrun{
path <- here::here("inst/extdata/tool1")
# demo filter + tidy
x <- Tool1$new(path = path)$
  filter_files(exclude = "alignments_dupfreq")$
  tidy(keep_raw = TRUE)
x$tbls
x$files
x$list_files()
lx <- Linx$new(path)
dbconn <- DBI::dbConnect(
  drv = RPostgres::Postgres(),
  dbname = "nemo",
  user = "orcabus"
)
lx$nemofy(
    diro = "nogit/test_data",
    format = "db", # "parquet",
    id = "run2",
    dbconn = dbconn,
    include = NULL,
    exclude = NULL
)
DBI::dbDisconnect(dbconn)
} # }