bedtools_nuc: bedtools_nuc
In HelloRanges: Introduce *Ranges to bedtools users

Description Usage Arguments Details Value Author(s) References See Also Examples

Summarize DNA sequences over the specified ranges.

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    bedtools_nuc(cmd = "--help")
    R_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = FALSE)
    do_bedtools_nuc(fi, bed, s = FALSE, pattern = NULL, fullHeader = FALSE)

`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.
`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.
`pattern`	Optional sequence pattern to count in each subsequence.
`fullHeader`	Use the full FASTA header as the names. By default, use just the first word.

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

bedtools_nuc: Parses the bedtools command line and compiles it to the equivalent R code.
R_bedtools_nuc: Accepts R arguments corresponding to the command line arguments and compiles the equivalent R code.
do_bedtools_nuc: Evaluates the result of R_bedtools_nuc. Recommended only for demonstration and testing. It is best to integrate the compiled code into an R script, after studying it.

Computes AT/GC percentage and counts each type of base. Relies on Biostrings utilities like letterFrequency and alphabetFrequency. The counting of pattern occurrences uses vcountPattern.

A language object containing the compiled R code, evaluating to a DataFrame with summary statistics including the AC and GT percentage, and the counts of each type of base. Also includes the count of pattern, if specified.

Michael Lawrence

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

letterFrequency for summarizing sequences, matchPattern for pattern matching.

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

## End(Not run)
    ## default behavior, note the two dashes in '--fi'
    bedtools_nuc("--fi test.fasta -bed a.bed")
    ## with pattern counting
    bedtools_nuc("--fi test.fasta -bed a.bed -pattern ATA")