exporting AAstringset as fasta file

Question

[Avner]

Hi

I have AAstringset which I like to save as multiple alignment FASTA. my goal is to present the amino acid alignment in a clear way.

I tried:

aminoset <- AlignTranslation(DNA_seq_set, type="AAStringSet") #this works great 
writeXStringSet(aminoset ,file="protein Alignment.fa") # this end up in an empty file

Any suggestions?

Answer 1

[pgp.martin]

For me this works:

library(DECIPHER)
fas <- system.file("extdata", "50S_ribosomal_protein_L2.fas", package="DECIPHER")
dna <- readDNAStringSet(fas)
aminoset <- AlignTranslation(dna, type="AAStringSet")
writeXStringSet(aminoset ,file="proteinAlignment.fa")

The fasta file is not empty