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\name{FaInput}
\Rdversion{1.1}
\alias{indexFa}
\alias{indexFa,character-method}
\alias{scanFaIndex}
\alias{scanFaIndex,character-method}
\alias{countFa}
\alias{countFa,character-method}
\alias{scanFa}
\alias{scanFa,character,GRanges-method}
\alias{scanFa,character,RangesList-method}
\alias{scanFa,character,RangedData-method}
\alias{scanFa,character,missing-method}
\title{
Operations on indexed 'fasta' files.
}
\description{
Scan indexed fasta (or compressed fasta) files and their indicies.
}
\usage{
indexFa(file, ...)
\S4method{indexFa}{character}(file, ...)
scanFaIndex(file, ...)
\S4method{scanFaIndex}{character}(file, ...)
countFa(file, ...)
\S4method{countFa}{character}(file, ...)
scanFa(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
\S4method{scanFa}{character,GRanges}(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
\S4method{scanFa}{character,RangesList}(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
\S4method{scanFa}{character,RangedData}(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
\S4method{scanFa}{character,missing}(file, param, ...,
as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
}
\arguments{
\item{file}{A character(1) vector containing the fasta file path.}
\item{param}{An optional \code{\linkS4class{GRanges}},
\code{\linkS4class{RangesList}}, or \code{\linkS4class{RangedData}}
instance to select reads (and sub-sequences) for input.}
\item{as}{A character(1) vector indicating the type of object to
return; default \code{DNAStringSet}.}
\item{...}{Additional arguments, passed to \code{readDNAStringSet} /
\code{readRNAStringSet} / \code{readAAStringSet} when \code{param}
is \sQuote{missing}.}
}
\value{
\code{indexFa} visits the path in \code{file} and create an index file
at the same location but with extension \sQuote{.fai}).
\code{scanFaIndex} reads the sequence names and and widths of recorded
in an indexed fasta file, returning the information as a
\code{\linkS4class{GRanges}} object.
\code{countFa} returns the number of records in the fasta file.
\code{scanFa} return the sequences indicated by \code{param} as a
\code{\linkS4class{DNAStringSet}}, \code{\linkS4class{RNAStringSet}},
\code{\linkS4class{AAStringSet}} instance. \code{seqnames(param)}
selects the sequences to return; \code{start(param)} and
\code{end{param}} define the (1-based) region of the sequence to
return. Values of \code{end(param)} greater than the width of the
sequence are set to the width of the sequence. When \code{param} is
missing, all records are selected. When \code{param} is
\code{GRanges()}, no records are selected.
}
\references{
\url{http://samtools.sourceforge.net/} provides information on
\code{samtools}.
}
\author{
Martin Morgan <mtmorgan@fhcrc.org>.
}
\examples{
fa <- system.file("extdata", "ce2dict1.fa", package="Rsamtools",
mustWork=TRUE)
countFa(fa)
(idx <- scanFaIndex(fa))
(dna <- scanFa(fa, idx[1:2]))
ranges(idx) <- narrow(ranges(idx), -10) # last 10 nucleotides
(dna <- scanFa(fa, idx[1:2]))
}
\keyword{ manip }
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