| read.fasta {seqinr} | R Documentation |
Read nucleic or amino-acid sequences from a file in FASTA format.
read.fasta(file = system.file("sequences/ct.fasta", package = "seqinr"),
seqtype = c("DNA", "AA"), File = NULL, as.string = FALSE, forceDNAtolower = TRUE,
set.attributes = TRUE, legacy.mode = TRUE, seqonly = FALSE, strip.desc = FALSE,
bfa = FALSE, sizeof.longlong = .Machine$sizeof.longlong,
endian = .Platform$endian, apply.mask = TRUE)
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 file which is present in the sequences folder
of the seqinR package. |
seqtype |
the nature of the sequence: DNA or AA, defaulting
to DNA |
File |
Synonymous of file. As from seqinR >= 1.1-3 this argument is deprecated and a warning is issued |
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 |
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. |
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.
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 (http://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.
By default read.fasta return a list of vector of chars. Each element
is a sequence object of the class SeqFastadna or SeqFastaAA.
D. Charif, J.R. Lobry
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
FIXME: a reference to MAQ when published.
citation("seqinr")
write.fasta to write sequences in a FASTA file,
gb2fasta to convert a GenBank file into a FASTA file,
read.alignment to read aligned sequences,
reverse.align to get an alignment at the nucleic level from the
one at the amino-acid level
#
# 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*")
#
# 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$sizeof.longlong == 8
#
fastafile <- system.file("sequences/ct.fasta", package = "seqinr")
bfafile <- system.file("sequences/ct.bfa", package = "seqinr")
original <- read.fasta(fastafile, as.string = TRUE, set.att = FALSE)
bfavers <- read.fasta(bfafile, as.string = TRUE, set.att = FALSE, bfa = TRUE,
endian = "little", sizeof.longlong = 8)
if(!identical(original, bfavers)){
warning(paste("trouble reading bfa file with endian =", .Platform$endian,
"and sizeof.longlong =", .Machine$sizeof.longlong))
}