seqinr (version 4.2-36)

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)

Value

none

Arguments

source.file

GenBank file

destination.file

Fasta file

Author

J.R. Lobry

Details

Multiple entries in GenBank file are not supported.

References

citation("seqinr")

See Also

oriloc

Examples

  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"
  #