| read.fasta {seqinr} | R Documentation |
Read sequences from a file in FASTA format.
read.fasta(file = system.file("sequences/ct.fasta", package = "seqinr"),
seqtype = "DNA", File = NULL, as.string = FALSE, forceDNAtolower = TRUE,
set.attributes = TRUE)
file |
The name of the file which the sequences in fasta format are to be read from |
seqtype |
the nature of the sequence: DNA or AA |
File |
Synonymous of file. Maintained for upper compatibility with code based on seqinR <= 1.0-4 |
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 |
FASTA is a widely used format in biology, some FASTA files are distributed with the seqinr package, see the examples section bellow.
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
citation("seqinr")
#
# 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)