bedtools_getfasta {HelloRanges} | R Documentation

## bedtools_getfasta

### Description

Query sequence from a FASTA file given a set of ranges, including compound regions like transcripts and junction reads. This assumes the sequence is DNA.

### Usage

        bedtools_getfasta(cmd = "--help")
        R_bedtools_getfasta(fi, bed, s = FALSE, split = FALSE)
        do_bedtools_getfasta(fi, bed, s = FALSE, split = FALSE)

### Arguments

`cmd` | String of bedtools command line arguments, as they would be entered at the shell. There are a few incompatibilities between the docopt parser and the bedtools style. See argument parsing.
`fi` | Path to a FASTA file, or an XStringSet object.
`bed` | Path to a BAM/BED/GFF/VCF/etc file, a BED stream, a file object, or a ranged data structure, such as a GRanges, as the query. Use `"stdin"` for input from another process (presumably while running via `Rscript`). For streaming from a subprocess, prefix the command string with “<”, e.g., `"<grep foo file.bed"`. Any streamed data is assumed to be in BED format.
`s` | Force strandedness. If the feature occupies the antisense strand, the sequence will be reverse complemented.
`split` | Given BED12 or BAM input, extract and concatenate the sequences from the blocks (e.g., exons).

### Details

As with all commands, there are three interfaces to the `getfasta` command:

`bedtools_getfasta`

  Parses the bedtools command line and compiles it to the equivalent R code.

`R_bedtools_getfasta`

  Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.

`do_bedtools_getfasta`

  Evaluates the result of `R_bedtools_getfasta`. Recommended only for demonstration and testing. It is best to integrate the compiled code into an R script, after studying it.

It is recommended to retrieve reference sequence using a BSgenome package, either custom or provided by Bioconductor. Call `getSeq` to query for specific regions of the BSgenome object. If one must access a file, consider converting it to 2bit or FA (razip) format for indexed access using `import` and its `which` argument.

But if one must access a FASTA file, we need to read all of it with `readDNAStringSet` and extract regions using `x[gr]`, where `gr` is a GRanges or GRangesList.

### Value

A language object containing the compiled R code, evaluating to a DNAStringSet object.

### Author(s)

Michael Lawrence

### References

http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

### See Also

getSeq, the primary sequence query interface.

### Examples

    ## Not run:
    setwd(system.file("unitTests", "data", "getfasta", package="HelloRanges"))

    ## End(Not run)
        ## simple query
        bedtools_getfasta("--fi t.fa -bed blocks.bed")
        ## get spliced transcript/read sequence
        bedtools_getfasta("--fi t.fa -bed blocks.bed -split")

[Package HelloRanges version 1.18.0 Index]