seqinr (version 1.0-6)

read.fasta: read FASTA formatted files

Description

Read sequences from a file in FASTA format.

Usage

read.fasta(file = system.file("sequences/ct.fasta", package = "seqinr"), 
  seqtype = "DNA", File = NULL, as.string = FALSE, forceDNAtolower = TRUE,
  set.attributes = TRUE)

Arguments

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

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

Value

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

Details

FASTA is a widely used format in biology, some FASTA files are distributed with the seqinr package, see the examples section bellow.

References

citation("seqinr")

See Also

write.fasta, read.alignment

Examples

#
# 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)