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.ebi.ac.uk/help/formats_frame.html.

Author(s)

Barry Grant

References

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

See Also

read.fasta, read.fasta.pdb

Examples

## Read a PDB file
pdb <- read.pdb(system.file("examples/1bg2.pdb", package="bio3d"))

## 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" )

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

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

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

## Cut all but positions 330 to 345
aln$ali=aln$ali[,330:345]

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


[Package bio3d version 1.0-5 Index]