Write FASTA Formated Sequences

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

write.fasta(alignment=NULL, ids=NULL, seqs=alignment$ali, gap=TRUE, 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
gap	logical, if FALSE gaps will be removed.
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.

References

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

Author

Barry Grant

Note

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

See also

read.fasta, read.fasta.pdb

Examples

# \donttest{
# PDB server connection required - testing excluded

## Read a PDB file
pdb <- read.pdb("1bg2")
#>   Note: Accessing on-line PDB file
#> Warning: /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/1bg2.pdb  exists. Skipping download

## 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") )
#> 
#> See the output files:
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/eg.fa
#> /var/folders/xf/qznxnpf91vb1wm4xwgnbt0xr0000gn/T//Rtmp9oBdbc/eg2.fa
# }