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kmeRtone (version 1.0)

NCBI_Genome: Class constructor - build NCBI Genome object

Description

Class constructor - build NCBI Genome object

Class constructor - build NCBI Genome object

Arguments

Public fields

fasta_file

A path to FASTA file. fasta files.

genome_name

A genome name.

db

NCBI database: "refseq" or "genbank"

seq

A chromosome-named list of sequences.

seq_len

A chromosome-named vector of sequence length.

load_limit

Maximum chromosome sequences loaded.

mask

Genome mask status: "hard", "soft", or "none".

use_UCSC_name

Use UCSC style chromosome name? Default to FALSE.

headers

A chromosome-named vector of headers.

avail_seqs

Available chromosome sequences in the fasta file.

asm

Assembly summary.

Methods

Method new()

Create a new NCBI Genome class

Usage

NCBI_Genome$new(
  genome.name,
  db,
  fasta.file,
  asm,
  mask,
  use.UCSC.name,
  load.limit
)

Arguments

genome.name

A genome name. NCBI genome is included with kmeRtone.

db

NCBI database: "refseq" or "genbank".

fasta.file

A path to the NCBI-style fasta files. This is for user's own FASTA file.

asm

NCBI assembly summary.

mask

Genome mask status: "hard", "soft", or "none". Default is "none".

use.UCSC.name

Use UCSC style chromosome name? Default to FALSE.

load.limit

Maximum chromosome sequences loaded. Default is 1.

Returns

A new NCBI Genome object.

Method [()

Calling chromosome sequence by loading on demand. Maximum load is determine by load_limit field.

Usage

NCBI_Genome$[(chr.names, reload = FALSE)

Arguments

chr.names

Chromosome name. It can be a vector of chromosomes.

reload

Reload the sequence from the fasta_file. Default is FALSE.

Returns

A single or list of sequence of requested chromosome.

Method print()

Print summary of Genome object.

Usage

NCBI_Genome$print()

Returns

Message of Genome object summary.

Method get_assembly_report()

Get NCBI assembly report for the genome.

Usage

NCBI_Genome$get_assembly_report()

Returns

Message of Genome object summary.

Method clone()

The objects of this class are cloneable with this method.

Usage

NCBI_Genome$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Details

NCBI FASTA file contain nucleotide accession number at the headers, followed by some information about the sequence whether they are chromosome, plasmid, or mictochondria, their assembly status, etc.