bt.getfasta: Extract DNA sequences from a fasta file based on feature...
In PhanstielLab/bedtoolsr: Bedtools Wrapper

bt.getfasta

R Documentation

Extract DNA sequences from a fasta file based on feature coordinates.

Description

Extract DNA sequences from a fasta file based on feature coordinates.

Usage

bt.getfasta(
  fi,
  bed,
  fo = NULL,
  name = NULL,
  nameplus = NULL,
  nameOnly = NULL,
  split = NULL,
  tab = NULL,
  bedOut = NULL,
  s = NULL,
  fullHeader = NULL,
  rna = NULL,
  output = NULL
)

Arguments

`fi`	<fasta>
`bed`	<bed/gff/vcf>
`fo`	Output file (opt., default is STDOUT
`name`	Use the name field and coordinates for the FASTA header
`nameplus`	(deprecated) Use the name field and coordinates for the FASTA header
`nameOnly`	Use the name field for the FASTA header
`split`	Given BED12 fmt., extract and concatenate the sequences from the BED "blocks" (e.g., exons)
`tab`	Write output in TAB delimited format.
`bedOut`	Report extract sequences in a tab-delimited BED format instead of in FASTA format. - Default is FASTA format.
`s`	Force strandedness. If the feature occupies the antisense, strand, the sequence will be reverse complemented. - By default, strand information is ignored.
`fullHeader`	Use full fasta header. - By default, only the word before the first space or tab is used.
`rna`	The FASTA is RNA not DNA. Reverse complementation handled accordingly.
`output`	Output filepath instead of returning output in R.