Fasta: R6 Class for loading and analysing FASTA files

In sagrudd/floundeR: Toolkit For Nanopore Sequence Analysis

R6 Class for loading and analysing FASTA files

Description

This class aims to simplify the handling and exploration of FASTA files and provides simple methods for accessing information that can be used to assess bulk contents from a FASTA file - the analysis framework is provided by Rsamtools (alone).

Super class

floundeR::FloundeR -> Fasta

Active bindings

sequencingset

The sequencingset active binding returns a sequencingset object that is canonically structured around the passes_filtering logical field to allow assessment of sequencing characteristics.

Methods

Public methods

• Fasta$new()

• Fasta$sequence_chunks()

• Fasta$get_sequence_chunk()

• Fasta$get_tibble_chunk()

• Fasta$get_index()

• Fasta$count()

• Fasta$as_tibble()

• Fasta$clone()

Inherited methods

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

---

Method new()

Creates a new Fasta object. This initialisation method performs other sanity checking of the defined file(s) to ensure that it is indeed parseable and creates the required data structures.

Usage

Fasta$new(fasta_file)

Arguments

fasta_file

The source sequencing_summary file.

Returns

A new Fasta object.

Examples

canonical_fasta <- flnDr("cluster_cons.fasta.bgz")
fasta <- Fasta$new(canonical_fasta)

---

Method sequence_chunks()

Split the fasta sequence file explored by the package into sequence chunks for e.g. import into a relational database.

Usage

Fasta$sequence_chunks(chunk_size = 1000)

Arguments

chunk_size

The number of fasta entries that should be contained within a single chunk (default: 1000)

Returns

an invisible integer that defines the number of possible chunks; this can for example be iterated over

---

Method get_sequence_chunk()

Get a chunk of fasta sequences from a larger monolithic file

Usage

Fasta$get_sequence_chunk(id = 1)

Arguments

id

the chunk (see $sequence_chunks()) to extract sequence for - this must be an integer that is > 0 and <= sequence_chunks.

Returns

DNAStringSet containing the fasta entries corresponding to the specified sequence chunk.

---

Method get_tibble_chunk()

Get a chunk of fasta sequences from a larger monolithic file as a tibble

Usage

Fasta$get_tibble_chunk(id)

Arguments

id

the chunk (see $sequence_chunks()) to extract sequence for - this must be an integer that is > 0 and <= sequence_chunks.

Returns

tibble containing the fasta entries corresponding to the specified sequence chunk.

---

Method get_index()

return the Rsamtools FASTA index

Usage

Fasta$get_index()

Returns

GRanges object describing the fasta elements contained within the sequence file

---

Method count()

return the number of sequence elements contained within the sequence file specified

Usage

Fasta$count()

Returns

integer of fasta entries in file

---

Method as_tibble()

Export the imported dataset(s) as a tibble

The Fasta R6 object consumes a fasta format file and creates an object in memory that can be explored, sliced and filtered. This method dumps out the in-memory object for further exploration and development.

Usage

Fasta$as_tibble()

Returns

A tibble representation of the starting dataset

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Fasta$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Examples

## ------------------------------------------------
## Method `Fasta$new`
## ------------------------------------------------

canonical_fasta <- flnDr("cluster_cons.fasta.bgz")
fasta <- Fasta$new(canonical_fasta)

sagrudd/floundeR documentation built on Nov. 18, 2022, 10:31 a.m.