getFastaFromFolder {PhyloProfile} | R Documentation

## 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 tran@bio.uni-frankfurt.de

### 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)

[Package PhyloProfile version 1.4.11 Index]