getFastaFromFolder: Get fasta sequences

In BIONF/PhyloProfile: PhyloProfile

Get fasta sequences

Description

Get fasta sequences for the input phylogenetic profiles.

Usage

getFastaFromFolder(seqIDs = NULL, path = NULL, dirFormat = NULL,
    fileExt = NULL, idFormat = NULL)

Arguments

seqIDs	list of sequences IDs.
path	path to fasta folder.
dirFormat	directory format (either 1 for "path/speciesID.fa*" or 2 for "path/speciesID/speciesID.fa*")
fileExt	fasta file extension ("fa", "fasta", "fas" or "txt")
idFormat	fasta header format (1 for ">speciesID:seqID", 2 for ">speciesID@seqID", 3 for ">speciesID|seqID" or 4 for "seqID")

Value

A dataframe with one column contains sequences in fasta format.

Author(s)

Vinh Tran [e-mail]

See Also

mainLongRaw

Examples

seqIDs <- "RAT@10116@1|D3ZUE4"
path <- system.file(
    "extdata", "fastaFiles", package = "PhyloProfile", mustWork = TRUE
)
dirFormat <- 1
fileExt <- "fa"
idFormat <- 3
getFastaFromFolder(seqIDs, path, dirFormat, fileExt, idFormat)

BIONF/PhyloProfile documentation built on Dec. 18, 2024, 7:33 a.m.