readFASTA {Biostrings} | R Documentation |
FASTA is a simple file format for biological sequence data. A file may
contain one or more sequences, for each sequence there is a description
line which begins with a >
.
fasta.info(file, use.descs=TRUE) readFASTA(file, checkComments=TRUE, strip.descs=TRUE) writeFASTA(x, file="", width=80)
file |
Either a character string naming a file or a connection open
for reading or writing.
If "" (the default for writeFASTA ),
then the function writes to the standard output connection (the console)
unless redirected by sink .
|
use.descs |
TRUE or FALSE . Whether or not the description lines should
be used to name the elements of the returned integer vector.
|
checkComments |
Whether or not comments, lines beginning with a semi-colon should be found and removed. |
strip.descs |
Whether or not the ">" marking the beginning of the description
lines should be removed. Note that this argument is new
in Biostrings >= 2.8. In previous versions readFASTA
was keeping the ">".
|
x |
A list as one returned by readFASTA .
|
width |
The maximum number of letters per line of sequence. |
FASTA is a widely used format in biology. It is a relatively simple markup. I am not aware of a standard. It might be nice to check to see if the data that were parsed are sequences of some appropriate type, but without a standard that does not seem possible.
There are many other packages that provide similar, but different capabilities. The one in the package seqinr seems most similar but they separate the biological sequence into single character strings, which is too inefficient for large problems.
An integer vector (for fasta.info
) or a list (for readFASTA
)
with one element for each sequence in the file.
For readFASTA
, the elements are in two parts, one the description
and the second a character string of the biological sequence.
R. Gentleman, H. Pages
read.BStringSet
,
read.DNAStringSet
,
read.RNAStringSet
,
read.AAStringSet
,
write.XStringSet
,
read.table
,
scan
,
write.table
f1 <- system.file("extdata", "someORF.fa", package="Biostrings") file.info(f1) ff <- readFASTA(f1, strip.descs=TRUE) desc <- sapply(ff, function(x) x$desc) ## Keep the "reverse complement" sequences only ff2 <- ff[grep("reverse complement", desc, fixed=TRUE)] writeFASTA(ff2, file.path(tempdir(), "someORF2.fa"))