get.phylip.name: get the names of sequences from a PHYLIP file

In helixcn/phylotools: Phylogenetic Tools for Eco-Phylogenetics

get the names of sequences from a PHYLIP file

Description

get the names of sequences from a PHYLIP file.

Usage

get.phylip.name(infile, clean_name = FALSE)

Arguments

infile	character representing the name or path of the phylip file.
clean_name	logical, representing cleaning of the names will be performed.

Details

Punctuation characters and white space be replaced by "_". Definition of Punctuation characters can be found at regex.

Value

a character vector of the names of the sequences

Author(s)

Jinlong Zhang <[e-mail]>

See Also

read.phylip, regex

Examples

  cat("6 22",
  "seq_1    --TTACAAATTGACTTATTATA",
  "seq_2    GATTACAAATTGACTTATTATA",
  "seq_3    GATTACAAATTGACTTATTATA",
  "seq_5    GATTACAAATTGACTTATTATA",
  "seq_8    GATTACAAATTGACTTATTATA",
  "seq_10   ---TACAAATTGAATTATTATA",
  file = "matk.phy", sep = "\n")
get.phylip.name("matk.phy")
unlink("matk.phy")

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