R6 Class for loading and analysing Genbank whole genome files

This class aims to implement a couple of trivial methods for wrangling whole microbial genome information from Genbank files

Super class

floundeR::FloundeR -> GenbankGenome

Methods

Public methods

• GenbankGenome$new()

• GenbankGenome$list_cds()

• GenbankGenome$get_cds()

• GenbankGenome$focus_cds()

• GenbankGenome$focus_range()

• GenbankGenome$as_tibble()

• GenbankGenome$whole_genome_focus()

• GenbankGenome$focus_nucleotide()

• GenbankGenome$focus_codon()

• GenbankGenome$get_nucleotide()

• GenbankGenome$unfocus()

• GenbankGenome$is_focused()

• GenbankGenome$get_focus()

• GenbankGenome$clone()

Inherited methods

• floundeR::FloundeR$bin_data()
• floundeR::FloundeR$num_scale()
• floundeR::FloundeR$nums_scale()
• floundeR::FloundeR$print()

---

Method new()

Creates a new GenbankGenome object. This initialisation method performs minimal sanity checking of the defined file(s)

Usage

GenbankGenome$new(gb_file)

Arguments

gb_file

The source sequencing_summary file.

Returns

A new GenbankGenome object.

Examples

TB_reference = flnDr("TB_H37Rv.gb.gz")
tb <- GenbankGenome$new(TB_reference)

---

Method list_cds()

exports the annotated genomic features as a GenomicRanges object. This can be used for the review of content in a genomics context.

Usage

GenbankGenome$list_cds()

---

Method get_cds()

Get the CDS information for one or more annotated features from the genome of interest.

Usage

GenbankGenome$get_cds(feature_id = "fusA1")

---

Method focus_cds()

Usage

GenbankGenome$focus_cds(feature_id = "fusA1")

---

Method focus_range()

Usage

GenbankGenome$focus_range(chromosome = NULL, start = NULL, end = NULL)

---

Method as_tibble()

Usage

GenbankGenome$as_tibble()

---

Method whole_genome_focus()

Usage

GenbankGenome$whole_genome_focus()

---

Method focus_nucleotide()

Usage

GenbankGenome$focus_nucleotide(position)

---

Method focus_codon()

Usage

GenbankGenome$focus_codon(codon)

---

Method get_nucleotide()

Usage

GenbankGenome$get_nucleotide(position, strand)

---

Method unfocus()

Usage

GenbankGenome$unfocus()

---

Method is_focused()

Usage

GenbankGenome$is_focused()

---

Method get_focus()

Usage

GenbankGenome$get_focus()

---

Method clone()

The objects of this class are cloneable with this method.

Usage

GenbankGenome$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `GenbankGenome$new`
## ------------------------------------------------

TB_reference = flnDr("TB_H37Rv.gb.gz")
tb <- GenbankGenome$new(TB_reference)
#> ℹ Parsing genbank file [/private/var/folders/g5/kp9259xj7778b2kzcmym7jd00000gn/T/RtmpfBxQW1/temp_libpath10eeb6d0106e7/floundeR/extdata/TB_H37Rv.gb.gz]
#> → processing sequence [73527] lines
#> → setting sequence
#> ✔ Done! [213179] lines parsed