phylotools (version 0.2.2)

clean.fasta.name: Clean the name of a fasta file

Description

Cleaning the names of sequences for a fasta file. The punctuation characters and the white space will be replaced with "_".

Usage

clean.fasta.name(infile = NULL, outfile = "name_cleaned.fasta")

Arguments

infile

character string representing the name of the fasta file.

outfile

Character string representing the file name to be generated.

Value

This is a subroutine without a return value. A fasta file with all the names of sequences renamed will be saved to the working directory.

Details

Punctuation characters and white space will be replaced by "_". More information can be found at regex.

References

http://www.genomatix.de/online_help/help/sequence_formats.html

See Also

read.fasta

Examples

# NOT RUN {
  cat(
    ">seq_1*66",  "--TTACAAATTGACTTATTATA",
    ">seq_2()r",  "GATTACAAATTGACTTATTATA",
    ">seq_3:test",  "GATTACAAATTGACTTATTATA",
    ">seq_588",  "GATTACAAATTGACTTATTATA",
    ">seq_8$$yu",  "GATTACAAATTGACTTATTATA",
    ">seq_10", "---TACAAATTGAATTATTATA",
    file = "matk.fasta", sep = "\n")

  clean.fasta.name(infile = "matk.fasta")
  get.fasta.name("name_cleaned.fasta")

  # Delete file
  unlink("matk.fasta")
  unlink("name_cleaned.fasta")
# }