write.fasta {vcfR}

Create fasta format output

Description

Generate fasta format output

Usage

write.fasta(
  x,
  file = "",
  rowlength = 80,
  tolower = TRUE,
  verbose = TRUE,
  APPEND = FALSE,
  depr = TRUE
)

Arguments

x

object of class chromR

file

name for output file

rowlength

number of characters each row should not exceed

tolower

convert all characters to lowercase (T/F)

verbose

should verbose output be generated (T/F)

APPEND

should data be appended to an existing file (T/F)

depr

logical (T/F), this function has been deprecated, set to FALSE to override.

Details

The function write_fasta takes an object of class chromR and writes it to a fasta.gz (gzipped text) format file. The sequence in the seq slot of the chromR object is used to fill in the invariant sites. The parameter 'tolower', when set to TRUE, converts all the characters in teh sequence to lower case. This is important because some software, such as ape::DNAbin, requires sequences to be in lower case.