Conversion of GenBank file into fasta file
Converts a single entry in GenBank format into a fasta file.
gb2fasta(source.file, destination.file)
source.file |
GenBank file |
destination.file |
Fasta file |
Multiple entries in GenBank file are not supported.
none
J.R. Lobry
citation("seqinr")
myGenBankFile <- system.file("sequences/ct.gbk.gz", package = "seqinr")
#myFastaFileName <- "Acinetobacter_ADP1_uid61597.fasta"
myFastaFileName <-tempfile(pattern = "Acinetobacter_ADP1_uid61597",
tmpdir = tempdir(), fileext = "fasta")
tempdir(check = FALSE)
gb2fasta(myGenBankFile, myFastaFileName)
readLines(myFastaFileName)[1:5]
#
# Should be :
#
# [1] ">CHLTCG 1042519 bp"
# [2] "gcggccgcccgggaaattgctaaaagatgggagcaaagagttagagatctacaagataaa"
# [3] "ggtgctgcacgaaaattattaaatgatcctttaggccgacgaacacctaattatcagagc"
# [4] "aaaaatccaggtgagtatactgtagggaattccatgttttacgatggtcctcaggtagcg"
# [5] "aatctccagaacgtcgacactggtttttggctggacatgagcaatctctcagacgttgta"
#Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.