read_fasta: Read in a FASTA-formatted file containing DNA sequences

In phylotypr: Classifying DNA Sequences to Taxonomic Groupings

Read in a FASTA-formatted file containing DNA sequences

Description

Given a standard FASTA-formatted file, read_fasta will read in the contents of the file and create a three column data frame with columns for the sequence id, the sequence itself, and any comments found in the header line for each sequence.

Usage

read_fasta(file, degap = TRUE)

Arguments

file

Either a path to a file, a connection, or literal data (either a single string or a raw vector) containing DNA sequences in the standard FASTA format. There are no checks to determine whether the data are DNA or amino acid sequences. Files ending in .gz, .bz2, .xz, or .zip will be automatically uncompressed. Files starting with ⁠http://⁠, ⁠https://⁠, ⁠ftp://⁠, or ⁠ftps://⁠ will be automatically downloaded. Remote gz files can also be autom downloaded and decompressed.

degap

Logical value (default = TRUE) Removes gap characters from sequences indicated by "." or "-"

Value

A data frame object with three columns. The id column will contain the non-space characters following the > in the header line of each sequence; the sequence column will contain the sequence; and the comment column will contain any text found after the first whitespace character on the header line.

Note

The sequences in the FASTA file can have line breaks within them and read_fasta() will put those separate lines into the same sequence

Examples

temp <- tempfile()
write(">seqA\nATGCATGC\n>seqB\nTACGTACG", file = temp)
write(">seqC\nTCCGATGC", file = temp, append = TRUE)
write(">seqD B.ceresus UW85\nTCCGATGC", file = temp, append = TRUE)
write(">seq4\tE. coli K12\tBacteria;Proteobacteria;\nTCCGATGC",
  file = temp,
  append = TRUE
)
write(">seq_4\tSalmonella LT2\tBacteria;Proteobacteria;\nTCCGATGC",
  file = temp, append = TRUE
)
write(">seqE B.ceresus UW123\nTCCGATGC\nTCCGATGC",
  file = temp,
  append = TRUE
)

sequence_df <- read_fasta(temp)

phylotypr documentation built on April 3, 2025, 5:51 p.m.