getFastaFromFolder {PhyloProfile} | R Documentation |
Get fasta sequences for the input phylogenetic profiles.
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
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)