bt.getfasta: Extract DNA sequences from a fasta file based on feature...

View source: R/bt.getfasta.R

bt.getfastaR 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.


PhanstielLab/bedtoolsr documentation built on Aug. 29, 2024, 5:37 p.m.