getPacksFromFasta: Retrieve Saved packFinder Results (.fasta)

In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

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")
)

packFinder documentation built on Nov. 8, 2020, 5:24 p.m.