Operations on indexed 'fasta' files.

Description

Scan indexed fasta (or compressed fasta) files and their indicies.

Usage

indexFa(file, ...)
## S4 method for signature 'character'
indexFa(file, ...)

scanFaIndex(file, ...)
## S4 method for signature 'character'
scanFaIndex(file, ...)

countFa(file, ...)
## S4 method for signature 'character'
countFa(file, ...)

scanFa(file, param, ...)
## S4 method for signature 'character,GRanges'
scanFa(file, param, ...)
## S4 method for signature 'character,RangesList'
scanFa(file, param, ...)
## S4 method for signature 'character,RangedData'
scanFa(file, param, ...)
## S4 method for signature 'character,missing'
scanFa(file, param, ...)

Arguments

Value

indexFa visits the path in file and create an index file at the same location but with extension ‘.fai’).

scanFaIndex reads the sequence names and and widths of recorded in an indexed fasta file, returning the information as a GRanges object.

countFa returns the number of records in the fasta file.

scanFa return the sequences indicated by param as a DNAStringSet instance. seqnames(param) selects the sequences to return; start(param) and end{param} define the (1-based) region of the sequence to return. Values of end(param) greater than the width of the sequence are set to the width of the sequence. When param is missing, all records are selected. When param is GRanges(), no records are selected.

Author(s)

Martin Morgan <mtmorgan@fhcrc.org>.

References

http://samtools.sourceforge.net/ provides information on samtools.

Examples

fa <- system.file("extdata", "ce2dict1.fa", package="Rsamtools")
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]))