Save sq to fasta file

Writes sq objects with their names to a fasta file.

write_fasta(x, ...)

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

# S3 method for 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).

Value

No value is returned.

Details

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

See also

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

Examples

if (FALSE) {
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())
}

# 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())
#> Warning: Non-standard IUPAC symbols detected for DNA: 1549 characters were converted to N.
#> Error in UseMethod("mutate"): no applicable method for 'mutate' applied to an object of class "c('bioseq_dna', 'vctrs_vctr')"