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Parse a fasta file into a named character vector.

Source: R/read_fasta.r
read_fasta.Rd

Parse a fasta file into a named character vector.

Usage

read_fasta(file, ids = NULL)

Arguments

file

A file path, URL, or literal string with fasta-formatted sequences. Files can optionally be compressed with gzip or bzip2.

ids

Character vector of IDs to retrieve. The default, NULL, will retrieve everything.

Value

A named character vector in which names are the fasta headers (the text after > up to the first whitespace) and values are the sequences. Sequences spanning multiple lines are joined, and whitespace within sequences is removed.

Examples

    library(rbiom)

    fasta <- ">OTU1 first sequence\nATCG\nGGCC\n>OTU2\nTTAA\n"
    read_fasta(fasta)
#>       OTU1       OTU2 
#> "ATCGGGCC"     "TTAA" 

    outfile <- write_fasta(hmp50, tempfile(fileext = ".fna.gz"))
    seqs    <- read_fasta(outfile)
    unlink(outfile)

    identical(seqs, hmp50$sequences)
#> [1] TRUE