Read FASTA formated Sequences
Read aligned or un-aligned sequences from a FASTA format file.
read.fasta(file, rm.dup = TRUE, to.upper = FALSE, to.dash=TRUE)
file |
input sequence file. |
rm.dup |
logical, if TRUE duplicate sequences (with the same names/ids) will be removed. |
to.upper |
logical, if TRUE residues are forced to uppercase. |
to.dash |
logical, if TRUE ‘.’ gap characters are converted to ‘-’ gap characters. |
A list with two components:
ali |
an alignment character matrix with a row per sequence and a column per equivalent aminoacid/nucleotide. |
ids |
sequence names as identifers. |
call |
the matched call. |
For a description of FASTA format see: https://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml. When reading alignment files, the dash ‘-’ is interpreted as the gap character.
Barry Grant
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
# Read alignment
aln <- read.fasta(system.file("examples/hivp_xray.fa",package="bio3d"))
# Print alignment overview
aln
# Sequence names/ids
head( aln$id )
# Alignment positions 335 to 339
head( aln$ali[,33:39] )
# Sequence d2a4f_b
aa123( aln$ali["d2a4f_b",] )
# Write out positions 33 to 45 only
#aln$ali=aln$ali[,30:45]
#write.fasta(aln, file="eg2.fa")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.