apetools: Tools to Explore Files

In ape: Analyses of Phylogenetics and Evolution

Tools to Explore Files

Description

These functions help to find files on the local disk.

Usage

Xplorefiles(from = "HOME", recursive = TRUE, ignore.case = TRUE)
editFileExtensions()
bydir(x)
Xplor(from = "HOME")

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.

Xplor combines the other operations and opens the results in a Web browser with clickable links to the directories and files.

Value

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

Author(s)

Emmanuel Paradis

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
Xplor()

## End(Not run)

ape documentation built on May 29, 2024, 10:50 a.m.