apetools

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Tools to Explore Files

These functions help to find files on the local disk.

Keywords
manip
Usage
Xplorefiles(from = "HOME", recursive = TRUE, ignore.case = TRUE)
editFileExtensions()
bydir(x)
Arguments
from

the directory where to start the file search; by default, the `HOME' directory. Use from = getwd() to start from the current working directory.

recursive

whether to search the subdirectories; TRUE by default.

ignore.case

whether to ignore the case of the file extensions; TRUE by default.

x

a list returned by Xplorefiles.

Details

Xplorefiles looks for all files with a specified extension in their names. The default is to look for the following file types: CLUSTAL (.aln), FASTA (.fas, .fasta), FASTQ (.fq, .fastq), NEWICK (.nwk, .newick, .tre, .tree), NEXUS (.nex, .nexus), and PHYLIP (.phy). This list can be modified with editFileExtensions.

bydir sorts the list of files by directories.

Value

Xplorefiles returns a list. bydir prints the file listings on the console.

Aliases
  • apetools
  • Xplorefiles
  • editFileExtensions
  • bydir
Examples
# NOT RUN {
x <- Xplorefiles()
x # all data files on your disk
bydir(x) # sorted by directories
bydir(x["fasta"]) # only the FASTA files
Xplorefiles(getwd(), recursive = FALSE) # look only in current dir
# }
Documentation reproduced from package ape, version 4.1, License: GPL (>= 2)

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