convertAlign

Convert any format of DNA alignment into another format

catGenes::convertAlign()

Description

Convert one or multiple DNA alignments in FASTA, NEXUS or PHYLIP format into each other.

Arguments

Argument	Description
filepath	Path to the directory where the DNA alignments are stored.
format	Define either “NEXUS”, “FASTA” or “PHYLIP” format for writing the resulting newly converted files.
rmfiles	Logical, if TRUE, the original input file(s) are removed from the directory and only the newly converted files are kept.
dir	The path to the directory where the newly converted files should be saved. If no directory is given, then the files will saved in a subfolder named after the current date under the folder named RESULTS_convertAlign.

Examples

library(catGenes)

data(GenBank_accessions)

todaydate <- format(Sys.time(), "%d%b%Y")
folder_mined_seqs <- paste0("RESULTS_mineSeq/", todaydate)
folder_aligned_seqs <- paste0("RESULTS_alignSeqs/", todaydate)

mineSeq(inputdf = GenBank_accessions,
        gb.colnames = c("ITS", "matK"),
        as.character = FALSE,
        verbose = TRUE,
        save = TRUE,
        dir = "RESULTS_mineSeq",
        filename = "GenBanK_seqs")

alignSeqs(filepath = folder_mined_seqs,
          method = "ClustalW",
          gapOpening = "default",
          format = "NEXUS",
          verbose = TRUE,
          dir = "RESULTS_alignSeqs")

convertAlign(filepath = folder_aligned_seqs,
          format = "PHYLIP",
          rmfiles = FALSE,
          verbose = TRUE,
          dir = "RESULTS_convertAlign")