write_fasta: Save sq to fasta file

In tidysq: Tidy Processing and Analysis of Biological Sequences

Save sq to fasta file

Description

Writes sq objects with their names to a fasta file.

Usage

write_fasta(x, ...)

## S3 method for class 'sq'
write_fasta(
  x,
  name,
  file,
  width = 80,
  NA_letter = getOption("tidysq_NA_letter"),
  ...
)

## S3 method for class 'data.frame'
write_fasta(
  x,
  file,
  .sq = "sq",
  .name = "name",
  width = 80,
  NA_letter = getOption("tidysq_NA_letter"),
  ...
)

Arguments

x	[sq] An object this function is applied to.
...	further arguments to be passed from or to other methods.
name	[character] Vector of sequence names. Must be of the same length as sq object.
file	[character(1)] Absolute path to file to write to.
width	[integer(1)] Maximum number of characters to put in each line of file. Must be positive.
NA_letter	[character(1)] A string that is used to interpret and display NA value in the context of sq class. Default value equals to "!".
.sq	[character(1)] Name of a column that stores sequences.
.name	[character(1)] Name of a column that stores names (unique identifiers).

Details

Whenever a name has more letters than width parameter, nothing happens, as only sequences are split to fit within designated space.

Value

No value is returned.

See Also

Functions from output module: as.character.sq(), as.matrix.sq(), as.sq(), export_sq()

Examples

## Not run: 
sq_dna <- sq(c("ACTGCTG", "CTTAGA", "CCCT", "CTGAATGT"),
             alphabet = "dna_bsc")
write_fasta(sq_dna,
            c("bat", "cat", "rat", "elephant_swallowed_by_A_snake"),
            tempfile())

## End(Not run)

# It can be a part of tidyverse pipeline:
library(dplyr)
fasta_file <- system.file(package = "tidysq", "examples/example_aa.fasta")
read_fasta(fasta_file) %>%
  mutate(name = toupper(name)) %>%
  write_fasta(tempfile())

tidysq documentation built on April 12, 2025, 1:37 a.m.