write.fasta {bio3d}

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, 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.

Note

For a description of FASTA format see: https://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") )