getFastaFromFolder: Get fasta sequences
In PhyloProfile: PhyloProfile

Description Usage Arguments Value Author(s) See Also Examples

Get fasta sequences for the input phylogenetic profiles.

1 2	getFastaFromFolder(seqIDs = NULL, path = NULL, dirFormat = NULL, fileExt = NULL, idFormat = NULL)

`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")

A dataframe with one column contains sequences in fasta format.

Vinh Tran tran@bio.uni-frankfurt.de

mainLongRaw

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)