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)