\name{write2FASTA}
\alias{write2FASTA}
%- Also NEED an '\alias' for EACH other topic documented here.
\title{ write sequences to a file in fasta format}
\description{
  write the sequences obtained from getAllPeakSequence to a file in fasta format leveraging writeFASTA in Biostrings package. FASTA is a simple file format for biological sequence data. A FASTA format file contains one or more sequences and there is a header line which begins with a > proceeding each sequence.
}
\usage{
write2FASTA(mySeq, file="", width=80)
}
%- maybe also 'usage' for other objects documented here.
\arguments{
  \item{mySeq}{RangedData with varibles name and sequence ,e.g., results obtained from getAllPeakSequence} 
  \item{file}{Either a character string naming a file or a connection open for reading or writing. If "" (the default for write2FASTA), then the function writes to the standard output connection (the console) unless redirected by sink}
  \item{width}{ The maximum number of letters per line of sequence }
}
\details{
}
\value{
  Output as FASTA file format to the naming file or the console. 
}
\references{ }
\author{ Lihua Julie Zhu}
\note{
 
}
\seealso{  }
\examples{
peaksWithSequences = RangedData(IRanges(start=c(1000, 2000), end=c(1010, 2010), 
names=c("id1", "id2")), sequence= c("CCCCCCCCGGGGG", "TTTTTTTAAAAAA"))
write2FASTA(peaksWithSequences, file="testseq.fasta", width=50)
}
% Add one or more standard keywords, see file 'KEYWORDS' in the
% R documentation directory.
\keyword{ misc }