read.fasta {bio3d} | R Documentation |
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. |
For a description of FASTA format see: http://www.ebi.ac.uk/help/formats_frame.html. 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")) # Sequence names/ids aln$id # Alignment positions 335 to 339 aln$ali[,33:39] # Sequence d1bg2__ aln$ali["d2a4f_b",] # Write out positions 33 to 45 only #aln$ali=aln$ali[,30:45] #write.fasta(aln, file="eg2.fa")