seqinr (version 3.6-1)

gb2fasta: Conversion of GenBank file into fasta file

Description

Converts a single entry in GenBank format into a fasta file.

Usage

gb2fasta(source.file, destination.file)

Arguments

source.file

GenBank file

destination.file

Fasta file

Value

none

Details

Multiple entries in GenBank file are not supported.

References

citation("seqinr")

See Also

oriloc

Examples

Run this code
# NOT RUN {
  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"
  #
# }

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