R: Write FASTA Formated Sequences

write.fasta {bio3d} | R Documentation

## Write FASTA Formated Sequences

### Description

Write aligned or un-aligned sequences to a FASTA format file.

### Usage

    write.fasta(alignment=NULL, ids=NULL, seqs=alignment$ali, file, append = FALSE)

### Arguments

`alignment` | an alignment list object with `id` and `ali` components, similar to that generated by `read.fasta`.
`ids` | a vector of sequence names to serve as sequence identifers
`seqs` | an sequence or alignment character matrix or vector with a row per sequence
`file` | name of output file.
`append` | logical, if TRUE output will be appended to `file`; otherwise, it will overwrite the contents of `file`.

### Value

Called for its effect.

### Note

For a description of FASTA format see: http://www.ncbi.nlm.nih.gov/BLAST/blastcgihelp.shtml.

### Author(s)

Barry Grant

### References

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

### See Also

`read.fasta`, `read.fasta.pdb`

### Examples

    # PDB server connection required - testing excluded

    ## Read a PDB file
    pdb <- read.pdb("1bg2")

    ## Extract sequence from PDB file
    s <- aa321(pdb$seqres)                   # SEQRES
    a <- aa321(pdb$atom[pdb$calpha,"resid"]) # ATOM

    ## Write simple fasta file
    #write.fasta( seqs=seqbind(s,a), file="eg.fa")
    #write.fasta( ids=c("seqres","atom"), seqs=seqbind(s,a), file="eg.fa" )

    outfile1 = file.path(tempdir(), "eg.fa")
    write.fasta(list( id=c("seqres"),ali=s ), file = outfile1)
    write.fasta(list( id=c("atom"),ali=a ), file = outfile1, append=TRUE)

    ## Align seqres and atom records
    #seqaln(seqbind(s,a))

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

    ## Cut all but positions 130 to 245
    aln$ali=aln$ali[,130:245]

    outfile2 = file.path(tempdir(), "eg2.fa")
    write.fasta(aln, file = outfile2)

    invisible( cat("\nSee the output files:", outfile1, outfile2, sep="\n") )

[Package bio3d version 2.3-4 Index]