XStringSet-io {Biostrings} | R Documentation |
Functions to read/write an XStringSet or XStringViews object from/to a file.
## 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)
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. |
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.
fasta.info
,
readFASTA
,
writeFASTA
,
XStringSet-class,
XStringViews-class,
BString-class,
DNAString-class,
RNAString-class,
AAString-class
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)'