read.fasta: read FASTA formatted files

Description

Read nucleic or amino-acid sequences from a file in FASTA format.

Usage

read.fasta(file = system.file("sequences/ct.fasta.gz", package = "seqinr"),
  seqtype = c("DNA", "AA"), as.string = FALSE, forceDNAtolower = TRUE,
  set.attributes = TRUE, legacy.mode = TRUE, seqonly = FALSE, strip.desc = FALSE,
  whole.header = FALSE,
  bfa = FALSE, sizeof.longlong = .Machine$sizeof.longlong,
  endian = .Platform$endian, apply.mask = TRUE)

Value

By default read.fasta return a list of vector of chars. Each element is a sequence object of the class SeqFastadna or SeqFastaAA.

Arguments

file: The name of the file which the sequences in fasta format are to be read from. If it does not contain an absolute or relative path, the file name is relative to the current working directory, getwd. The default here is to read the ct.fasta.gz file which is present in the sequences folder of the seqinR package.
seqtype: the nature of the sequence: DNA or AA, defaulting to DNA
as.string: if TRUE sequences are returned as a string instead of a vector of single characters
forceDNAtolower: whether sequences with seqtype == "DNA" should be returned as lower case letters
set.attributes: whether sequence attributes should be set
legacy.mode: if TRUE lines starting with a semicolon ';' are ignored
seqonly: if TRUE, only sequences as returned without attempt to modify them or to get their names and annotations (execution time is divided approximately by a factor 3)
strip.desc: if TRUE the '>' at the beginning of the description lines is removed in the annotations of the sequences
whole.header: if TRUE the whole header line, except the first '>' character, is kept for sequence name. If FALSE, the default, the name is truncated at the first space (" ") character.
bfa: logical. If TRUE the fasta file is in MAQ binary format (see details). Only for DNA sequences.
sizeof.longlong: the number of bytes in a C long long type. Only relevant for bfa = TRUE. See .Machine
endian: character string, "big" or "little", giving the endianness of the processor in use. Only relevant for bfa = TRUE. See .Platform
apply.mask: logical defaulting to TRUE. Only relevant for bfa = TRUE. When this flag is TRUE the mask in the MAQ binary format is used to replace non acgt characters in the sequence by the n character. For pure acgt sequences (without gaps or ambiguous bases) turning this to FALSE will save time.

Author

D. Charif, J.R. Lobry

Details

FASTA is a widely used format in biology, some FASTA files are distributed with the seqinr package, see the examples section below. Sequence in FASTA format begins with a single-line description (distinguished by a greater-than '>' symbol), followed by sequence data on the next lines. Lines starting by a semicolon ';' are ignored, as in the original FASTA program (Pearson and Lipman 1988). The sequence name is just after the '>' up to the next space ' ' character, trailling infos are ignored for the name but saved in the annotations.

There is no standard file extension name for a FASTA file. Commonly found values are .fasta, .fas, .fa and .seq for generic FASTA files. More specific file extension names are also used for fasta sequence alignement (.fsa), fasta nucleic acid (.fna), fasta functional nucleotide (.ffn), fasta amino acid (.faa), multiple protein fasta (.mpfa), fasta RNA non-coding (.frn).

The MAQ fasta binary format was introduced in seqinR 1.1-7 and has not been extensively tested. This format is used in the MAQ (Mapping and Assembly with Qualities) software (https://maq.sourceforge.net/). In this format the four nucleotides are coded with two bits and the sequence is stored as a vector of C unsigned long long. There is in addition a mask to locate non-acgt characters.

References

Pearson, W.R. and Lipman, D.J. (1988) Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85:2444-2448

According to MAQ's FAQ page https://maq.sourceforge.net/faq.shtml last consulted 2016-06-07 the MAQ manuscript has not been published.

citation("seqinr")

Examples

Run this code

#
# Simple sanity check with a small FASTA file:
#
  smallFastaFile <- system.file("sequences/smallAA.fasta", package = "seqinr")
  mySmallProtein <- read.fasta(file = smallFastaFile, as.string = TRUE, seqtype = "AA")[[1]]
  stopifnot(mySmallProtein == "SEQINRSEQINRSEQINRSEQINR*")
#
# Simple sanity check with the gzipped version of the same small FASTA file:
#
  smallFastaFile <- system.file("sequences/smallAA.fasta.gz", package = "seqinr")
  mySmallProtein <- read.fasta(file = smallFastaFile, as.string = TRUE, seqtype = "AA")[[1]]
  stopifnot(mySmallProtein == "SEQINRSEQINRSEQINRSEQINR*")
#
# Example of a DNA file in FASTA format:
#
  dnafile <- system.file("sequences/malM.fasta", package = "seqinr")
#
# Read with defaults arguments, looks like:
#
# $XYLEECOM.MALM
# [1] "a" "t" "g" "a" "a" "a" "a" "t" "g" "a" "a" "t" "a" "a" "a" "a" "g" "t"
# ...
  read.fasta(file = dnafile)
#
# The same but do not turn the sequence into a vector of single characters, looks like:
#
# $XYLEECOM.MALM
# [1] "atgaaaatgaataaaagtctcatcgtcctctgtttatcagcagggttactggcaagcgc
# ...
  read.fasta(file = dnafile, as.string = TRUE)
#
# The same but do not force lower case letters, looks like:
#
# $XYLEECOM.MALM
# [1] "ATGAAAATGAATAAAAGTCTCATCGTCCTCTGTTTATCAGCAGGGTTACTGGCAAGC
# ...
  read.fasta(file = dnafile, as.string = TRUE, forceDNAtolower = FALSE)
#
# Example of a protein file in FASTA format:
#
  aafile <- system.file("sequences/seqAA.fasta", package = "seqinr")
#
# Read the protein sequence file, looks like:
#
# $A06852
# [1] "M" "P" "R" "L" "F" "S" "Y" "L" "L" "G" "V" "W" "L" "L" "L" "S" "Q" "L"
# ...
  read.fasta(aafile, seqtype = "AA")
#
# The same, but as string and without attributes, looks like:
#
# $A06852
# [1] "MPRLFSYLLGVWLLLSQLPREIPGQSTNDFIKACGRELVRLWVEICGSVSWGRTALSLEEP
# QLETGPPAETMPSSITKDAEILKMMLEFVPNLPQELKATLSERQPSLRELQQSASKDSNLNFEEFK
# KIILNRQNEAEDKSLLELKNLGLDKHSRKKRLFRMTLSEKCCQVGCIRKDIARLC*"
#
  read.fasta(aafile, seqtype = "AA", as.string = TRUE, set.attributes = FALSE)
#
# Example with a FASTA file that contains comment lines starting with
# a semicolon character ';'
#
  legacyfile <- system.file("sequences/legacy.fasta", package = "seqinr")
  legacyseq <- read.fasta(file = legacyfile, as.string = TRUE)
  stopifnot( nchar(legacyseq) == 921 )
#
# Example of a MAQ binary fasta file produced with maq fasta2bfa ct.fasta ct.bfa
# on a platform where .Platform$endian == "little" and .Machine$sizeof.longlong == 8
#
  fastafile <- system.file("sequences/ct.fasta.gz", package = "seqinr")
  bfafile <- system.file("sequences/ct.bfa", package = "seqinr")

  original <- read.fasta(fastafile, as.string = TRUE, set.att = FALSE)
  bfavers <- read.fasta(bfafile, as.string = TRUE, set.att = FALSE, bfa = TRUE,
    endian = "little", sizeof.longlong = 8)
  if(!identical(original, bfavers)){
     warning(paste("trouble reading bfa file on a platform with endian =",
     .Platform$endian, "and sizeof.longlong =", .Machine$sizeof.longlong))
  }

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