XStringSet-io {Biostrings}R Documentation

Read/write an XStringSet or XStringViews object from/to a file

Description

Functions to read/write an XStringSet or XStringViews object from/to a file.

Usage

  ## XStringSet object
  read.BStringSet(file, format)
  read.DNAStringSet(file, format)
  read.RNAStringSet(file, format)
  read.AAStringSet(file, format)
  write.XStringSet(x, file="", format, width=80)

  ## XStringViews object
  read.XStringViews(file, format, subjectClass, collapse="")
  write.XStringViews(x, file="", format, width=80)

  ## Some related helper functions
  FASTArecordsToCharacter(FASTArecs, use.names=TRUE)
  CharacterToFASTArecords(x)
  FASTArecordsToXStringViews(FASTArecs, subjectClass, collapse="")
  XStringSetToFASTArecords(x)

Arguments

file Either a character string naming a file or a connection open for reading or writing. If "" (the default for write.XStringSet and write.XStringViews), then the functions write to the standard output connection (the console) unless redirected by sink.
format Only "fasta" is supported for now.
x For write.XStringSet and write.XStringViews, the object to write to file. For CharacterToFASTArecords, the (possibly named) character vector to be converted to a list of FASTA records as one returned by readFASTA. For XStringSetToFASTArecords, the XStringSet object to be converted to a list of FASTA records as one returned by readFASTA.
width Only relevant if format is "fasta". The maximum number of letters per line of sequence.
subjectClass The class to be given to the subject of the XStringViews object created and returned by the function. Must be the name of one of the direct XString subtypes i.e. "BString", "DNAString", "RNAString" or "AAString".
collapse An optional character string to be inserted between the views of the XStringViews object created and returned by the function.
FASTArecs A list of FASTA records as one returned by readFASTA.
use.names Whether or not the description line preceding each FASTA records should be used to set the names of the returned vector.

Details

Only FASTA files are supported for now.

Reading functions read.BStringSet, read.DNAStringSet, read.RNAStringSet, read.AAStringSet and read.XStringViews load sequences from a file into an XStringSet or XStringViews object.

Writing functions write.XStringSet and write.XStringViews write an XStringSet or XStringViews object to a file or connection.

FASTArecordsToCharacter, CharacterToFASTArecords, FASTArecordsToXStringViews and XStringSetToFASTArecords are helper functions used internally by write.XStringSet and read.XStringViews for switching between different representations of the same object.

See Also

fasta.info, readFASTA, writeFASTA, XStringSet-class, XStringViews-class, BString-class, DNAString-class, RNAString-class, AAString-class

Examples

  file <- system.file("extdata", "someORF.fa", package="Biostrings")
  x <- read.DNAStringSet(file, "fasta")
  x
  write.XStringSet(x, format="fasta") # writes to the console

  ## Converting 'x'...
  ## ... to a list of FASTA records (as one returned by the "readFASTA" function)
  x1 <- XStringSetToFASTArecords(x)
  ## ... to a named character vector
  x2 <- FASTArecordsToCharacter(x1) # same as 'as.character(x)'

[Package Biostrings version 2.10.22 Index]