NAME
megatree-loader - Loads a Newick tree into a database or a spreadsheet
SYNOPSIS
megatree-loader -i <file> [-d <file>] [-vhm]OPTIONS
- -i <file> or -infile <file>
-
Input tree file in Newick format.
- -d <file> or -dbfile <file>
-
Optional.
Location of a database file, compatible with sqlite3, which will be produced. This file can not yet exist. If it does, an error message will be emitted and the program will quit.
If this argument is not provided, the tree topology will be emitted as a comma-separated spreadsheet. (In principle, this spreadsheet could subsequently be loaded into sqlite3 and then be further indexed by the API.)
- -v or -verbose
-
Optional.
With this option, more feedback messages are written during processing. This option can be used multiple times, which increases the verbosity further.
- -h or -help
-
Optional.
Prints help message / documentation.
- -m or -man
-
Optional.
Prints manual page. Additional information is available in the documentation, i.e.
perldoc megatree-loader
DESCRIPTION
This program produces a database file or a CSV spreadsheet from a (very large) Newick tree file. Such a database provides much quicker random access to immutable trees, such as very large metabarcoding trees, the NCBI taxonomy, etc. The example trees that are referred to by the release of Bio::Phylo::Forest::DBTree have been produced in this way. They can be accessed by an API that is compatible with Bio::Phylo, but much more scalable. An example of such API usage is presented by the megatree-pruner script.