print.fasta: Printing Sequence Alignments

In bio3d: Biological Structure Analysis

Printing Sequence Alignments

Description

Print method for fasta and pdbs sequence alignment objects.

Usage

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

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’.

Value

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

Author(s)

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)

bio3d documentation built on Oct. 30, 2024, 1:08 a.m.