R/MergeFasta.R

In TBradley27/filtar_R: A Series of Support Functions for the Main Filtar Workflow

#' Concatenate fasta seqeunce for fasta records with the same header. Concatenation occurs in order of appearance in the file 

#' @param file name of file containing fasta records
#' @return A one-column tibble in which fasta headers and fasta sequences are interleaved
#' @export
#' @importFrom plyr .

MergeFasta = function(file) {
  # A function which concatenates sequences (depending on order of appearance in fasta file) which are 
  # attributable to the same fasta header

  # Input:
  #   file: An unmered fasta file

  # Output:
  #   fasta: A merged fasta file

  fasta = readr::read_tsv(file, col_names=c("fasta_unicolumn"))

  header_records = grepl(">", fasta$fasta_unicolumn) # Boolean vector

  fasta_header = fasta[header_records,]
  fasta_seq = fasta[!header_records,]

  fasta = dplyr::bind_cols(fasta_header, fasta_seq) # Convert to a n x 2 data frame
  colnames(fasta) = c("header","seq")

  fasta = plyr::ddply(fasta, .(header), function(dat) { # The main functional code
    paste(dat$seq, collapse='')
  }  )

  colnames(fasta) = c("header","seq")

  fasta = tibble::as.tibble(fasta)

  fasta = c(t(fasta))   # Transpose data frame, so that data can be written in the correct format

  return(fasta)
}