getPacksFromFasta {packFinder} | R Documentation

## Retrieve Saved packFinder Results (.fasta)

### Description

Retrieves a dataframe of potential Pack-TYPE elements, previously saved using `packSearch` followed by `packsToFasta`. Parses the .fasta file and title field containing:

- seqnames - name of origin sequence

- start - transposon base start position on origin sequence

- end - transposon base end position on origin sequence

- width - width of transposon

- strand - direction of transposon ("+", "-" or "*")

- TSD - terminal site duplication (TSD) sequence

### Usage

    getPacksFromFasta(file)

### Arguments

`file` | Path to predicted transposons in FASTA format.

### Value

Dataframe in the format used by `packSearch`.

### Author(s)

Jack Gisby

### See Also

`packsToFasta`, `packSearch`

### Examples

    data(arabidopsisThalianaRefseq)
    data(packMatches)

    packMatches <- getPacksFromFasta(
        system.file("extdata", "packMatches.fasta", package = "packFinder")
    )

[Package packFinder version 1.4.0 Index]