clean.fasta.name: Clean the name of a fasta file
In helixcn/phylotools: Phylogenetic Tools for Eco-Phylogenetics

clean.fasta.name

R Documentation

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 <jinlongzhang01@gmail.com>

References

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

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")

helixcn/phylotools documentation built on Oct. 11, 2024, 4:11 a.m.