R: Read FASTA formated Sequences

read.fasta {bio3d} | R Documentation

## Read FASTA formated Sequences

### Description

Read aligned or un-aligned sequences from a FASTA format file.

### Usage

    read.fasta(file, rm.dup = TRUE, to.upper = FALSE, to.dash=TRUE)

### Arguments

`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.

### Value

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.

### Note

For a description of FASTA format see: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml. When reading alignment files, the dash ‘-’ is interpreted as the gap character.

### Author(s)

Barry Grant

### References

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

### See Also

`read.fasta.pdb`

### Examples

    # 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")

[Package bio3d version 2.3-3 Index]