fasta2nucleotideContent: Get sequence content from a single FASTA file.

In daewoooo/SVbyEye: Visualization of genomic structural variants

Get sequence content from a single FASTA file.

Description

This function with takes a path to FASTA file containing a single sequence and report counts and frequencies of user defined ‘sequence.pattern' (such as exact DNA pattern, e.g. ’GA') or 'nucleotide.content' (such as sequence GC content) across the whole sequence or in user defined bins.

Usage

fasta2nucleotideContent(
  fasta.seq = NULL,
  fasta.file = NULL,
  binsize = NULL,
  sequence.pattern = NULL,
  nucleotide.content = NULL
)

Arguments

fasta.seq	A DNAStringSet-class object containing a single FASTA sequence.
fasta.file	A path to a valid FASTA file to be processed.
binsize	A user defined number of base pairs to split the loaded FASTA sequence into
sequence.pattern	A user defined DNA sequence pattern which occurrences will be counted in submitted 'fasta.seq'. (e.g. set ‘sequence.pattern' to ’GA' to obtain counts of all 'GA' occurrences per FASTA sequence).
nucleotide.content	A user defined nucleotides which total content will be counted in submitted 'fasta.seq'. (e.g. to obtain 'GC' content set ‘nucleotide.content' to ’GC')

Value

A GRanges-class object with reported nucleotide content metacolumns

Author(s)

David Porubsky

Examples

## Get FASTA to process ##
asm.fasta <- system.file("extdata", "test_getFASTA_query.fasta", package = "SVbyEye")
## Report sequence content for a given FASTA file in 5000bp long bins
fasta2nucleotideContent(fasta.file = asm.fasta, binsize = 5000, sequence.pattern = "AT")

daewoooo/SVbyEye documentation built on Oct. 15, 2024, 6:12 a.m.