Read/write an ModStringSet object from/to a file

Functions to read/write an ModStringSet object from/to a file.

readModDNAStringSet(
  filepath,
  format = "fasta",
  nrec = -1L,
  skip = 0L,
  seek.first.rec = FALSE,
  use.names = TRUE,
  with.qualities = FALSE
)

readModRNAStringSet(
  filepath,
  format = "fasta",
  nrec = -1L,
  skip = 0L,
  seek.first.rec = FALSE,
  use.names = TRUE,
  with.qualities = FALSE
)

writeModStringSet(
  x,
  filepath,
  append = FALSE,
  compress = FALSE,
  compression_level = NA,
  format = "fasta",
  ...
)

Arguments

filepath, format, nrec, skip, seek.first.rec, use.names, with.qualities, append, compress, compression_level, ...

See XStringSet-io for more details.

x

A ModStringSet object.

Value

A ModStringSet of the defined type.

Examples

seqs <- paste0(paste(alphabet(ModDNAString()), collapse = ""),
               c("A","G","T"))
seqs
#> [1] "ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑\"√/≡ζ~A"
#> [2] "ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑\"√/≡ζ~G"
#> [3] "ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑\"√/≡ζ~T"

set <- ModDNAStringSet(seqs)
set
#>   A ModDNAStringSet instance of length 3
#>     width seq
#> [1]    56 ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑"√/≡ζ~A
#> [2]    56 ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑"√/≡ζ~G
#> [3]    56 ACGTN-+.pδO]DJeg`bU∝πI763218∉⊆⊇Rαmh×f4νX'κo()ηa⇓⇑"√/≡ζ~T

file <- tempfile()
writeModStringSet(set, file)
read <- readModDNAStringSet(file)
read
#>   A ModDNAStringSet instance of length 3
#>     width seq                                               names               
#> [1]    56 ACGTN-+.pδO]DJeg`bU∝πI7...mh×f4νX'κo()ηa⇓⇑"√/≡ζ~A 
#> [2]    56 ACGTN-+.pδO]DJeg`bU∝πI7...mh×f4νX'κo()ηa⇓⇑"√/≡ζ~G 
#> [3]    56 ACGTN-+.pδO]DJeg`bU∝πI7...mh×f4νX'κo()ηa⇓⇑"√/≡ζ~T