FaInput {Rsamtools} | R Documentation

## 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, ...,
        as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
    ## S4 method for signature 'character,GRanges'
    scanFa(file, param, ...,
        as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
    ## S4 method for signature 'character,IntegerRangesList'
    scanFa(file, param, ...,
        as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))
    ## S4 method for signature 'character,missing'
    scanFa(file, param, ...,
        as=c("DNAStringSet", "RNAStringSet", "AAStringSet"))

### Arguments

`file` | A character(1) vector containing the fasta file path.
`param` | An optional `GRanges` or `IntegerRangesList` instance to select reads (and sub-sequences) for input.
`as` | A character(1) vector indicating the type of object to return; default `DNAStringSet`.
`...` | Additional arguments, passed to `readDNAStringSet` / `readRNAStringSet` / `readAAStringSet` when `param` is ‘missing’.

### 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`, `RNAStringSet`, `AAStringSet` 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",
                      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]))

[Package Rsamtools version 2.6.0 Index]