Esvee Object

Esvee file parsing and manipulation.

Super class

nemo::Tool -> Esvee

Methods

Public methods

• Esvee$new()

• Esvee$parse_prepfraglen()

• Esvee$tidy_prepfraglen()

• Esvee$parse_prepdiscstats()

• Esvee$tidy_prepdiscstats()

• Esvee$parse_prepjunction()

• Esvee$tidy_prepjunction()

• Esvee$parse_assemblephased()

• Esvee$tidy_assemblephased()

• Esvee$parse_assembleassembly()

• Esvee$tidy_assembleassembly()

• Esvee$parse_assemblebreakend()

• Esvee$tidy_assemblebreakend()

• Esvee$parse_assemblealignment()

• Esvee$tidy_assemblealignment()

• Esvee$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()

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Method new()

Create a new Esvee object.

Usage

Esvee$new(path = NULL, files_tbl = NULL)

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().

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Method parse_prepfraglen()

Read prep.fragment_length.tsv file.

Usage

Esvee$parse_prepfraglen(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_prepfraglen()

Tidy prep.fragment_length.tsv file.

Usage

Esvee$tidy_prepfraglen(x)

Arguments

x

(character(1))
Path to file.

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Method parse_prepdiscstats()

Read prep.disc_stats.tsv file.

Usage

Esvee$parse_prepdiscstats(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_prepdiscstats()

Tidy prep.disc_stats.tsv file.

Usage

Esvee$tidy_prepdiscstats(x)

Arguments

x

(character(1))
Path to file.

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Method parse_prepjunction()

Read prep.junction.tsv file.

Usage

Esvee$parse_prepjunction(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_prepjunction()

Tidy prep.junction.tsv file.

Usage

Esvee$tidy_prepjunction(x)

Arguments

x

(character(1))
Path to file.

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Method parse_assemblephased()

Read esvee.phased_assembly.tsv file.

Usage

Esvee$parse_assemblephased(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_assemblephased()

Tidy esvee.phased_assembly.tsv file.

Usage

Esvee$tidy_assemblephased(x)

Arguments

x

(character(1))
Path to file.

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Method parse_assembleassembly()

Read esvee.assembly.tsv file.

Usage

Esvee$parse_assembleassembly(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_assembleassembly()

Tidy esvee.assembly.tsv file.

Usage

Esvee$tidy_assembleassembly(x)

Arguments

x

(character(1))
Path to file.

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Method parse_assemblebreakend()

Read breakend.tsv file.

Usage

Esvee$parse_assemblebreakend(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_assemblebreakend()

Tidy breakend.tsv file.

Usage

Esvee$tidy_assemblebreakend(x)

Arguments

x

(character(1))
Path to file.

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Method parse_assemblealignment()

Read alignment.tsv file.

Usage

Esvee$parse_assemblealignment(x)

Arguments

x

(character(1))
Path to file.

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Method tidy_assemblealignment()

Tidy alignment.tsv file.

Usage

Esvee$tidy_assemblealignment(x)

Arguments

x

(character(1))
Path to file.

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Method clone()

The objects of this class are cloneable with this method.

Usage

Esvee$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

cls <- Esvee
indir <- system.file("extdata/oa", package = "tidywigits")
odir <- tempdir()
id <- "esvee_run1"
obj <- cls$new(indir)
obj$nemofy(odir = odir, format = "parquet", id = id)
#> NULL
(lf <- list.files(odir, pattern = "cobalt.*parquet", full.names = FALSE))
#> character(0)
#TODO: add esvee test data