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exporting AAstringset as fasta file

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?

bioconductor decipher
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updated by pgp.martin • pgp.martin • written by Avner • Avner

1 answer

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

• 0 views • link
written by pgp.martin • pgp.martin

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