| BStringViews-io {Biostrings} | R Documentation |
Functions to create a BStringViews object by reading a file or to write a BStringViews object to a file.
read.BStringViews(file, format, subjectClass, collapse="") write.BStringViews(x, file="", format, width=80) FASTArecordsToCharacter(FASTArecs, use.names=TRUE) CharacterToFASTArecords(x) FASTArecordsToBStringViews(FASTArecs, subjectClass, collapse="") BStringViewsToFASTArecords(x)
file |
Either a character string naming a file or a connection open
for reading or writing.
If "" (the default for write.BStringViews),
write.BStringViews writes to the standard
output connection (the console) unless redirected by sink.
|
format |
Only "fasta" is supported for now.
|
subjectClass |
The class to be given to the subject of the BStringViews object
created and returned by the function.
Must be "BString" or one of its subclasses: "DNAString",
"RNAString" or "AAString".
|
collapse |
An optional character string to be inserted between the views of the BStringViews object created and returned by the function. |
x |
For write.BStringViews, the BStringViews object to be
written to file.
For CharacterToFASTArecords, the (possibly named) character
vector to be converted to a list of FASTA records as one returned
by readFASTA.
For BStringViewsToFASTArecords, the BStringViews 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.
|
FASTArecs |
A list of FASTA records as one returned by readFASTA.
|
use.names |
Whether or not the desc component of the FASTA records should be
used to set the names of the returned vector.
|
Only FASTA files are supported for now.
read.BStringViews creates a BStringViews object
by reading a file.
write.BStringViews writes a BStringViews object
to a file or connection.
FASTArecordsToCharacter, CharacterToFASTArecords,
FASTArecordsToBStringViews and BStringViewsToFASTArecords
are convenience functions used internally by read.BStringViews
and write.BStringViews for switching between different
representations of the same object.
readFASTA,
writeFASTA,
BStringViews-class,
BString-class,
DNAString-class,
RNAString-class,
AAString-class
file <- system.file("Exfiles", "someORF.fsa", package="Biostrings")
x <- read.BStringViews(file, "fasta", "DNAString")
write.BStringViews(x, format="fasta") # writes to the console
## Converting 'x'...
## ... to a list of FASTA records (as one returned by the "readFASTA" function)
x1 <- BStringViewsToFASTArecords(x)
## ... to a named character vector
x2 <- FASTArecordsToCharacter(x1) # same as 'as.character(x)'