clean.fasta.name {phylotools}

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.

Details

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

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.

Author(s)

Jinlong Zhang <[e-mail]>

References

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

See Also

read.fasta

Examples

  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")