bio3d (version 2.4-4)

print.fasta: Printing Sequence Alignments

Description

Print method for fasta and pdbs sequence alignment objects.

Usage

# S3 method for fasta
print(x, alignment=TRUE, ...)
.print.fasta.ali(x, width = NULL, col.inds = NULL, numbers = TRUE,
         conservation=TRUE, ...)

Value

Called mostly for its effect but also silently returns block divided concatenated sequence strings as a matrix.

Arguments

x

a sequence alignment object as obtained from the functions read.fasta, read.fasta.pdb, pdbaln, seqaln, etc.

alignment

logical, if TRUE the sequence alignment will be printed to screen.

width

a single numeric value giving the number of residues per printed sequence block. By default this is determined from considering alignment identifier widths given a standard 85 column terminal window.

col.inds

an optional numeric vector that can be used to select subsets of alignment positions/columns for printing.

numbers

logical, if TRUE position numbers and a tick-mark every 10 positions are printed above and below sequence blocks.

conservation

logical, if TRUE conserved and semi-conserved columns in the alignment are marked with an ‘*’ and ‘^’, respectively.

...

additional arguments to ‘.print.fasta.ali’.

Author

Barry Grant

References

Grant, B.J. et al. (2006) Bioinformatics 22, 2695--2696.

See Also

read.fasta, read.fasta.pdb, pdbaln, seqaln

Examples

     file <- system.file("examples/kif1a.fa",package="bio3d")
     aln  <- read.fasta(file)
     print(aln)

     # print(aln, col.inds=30:100, numbers=FALSE)