NAME

megatree-bold-loader - Loads the processid taxonomy tree implied by a BOLD BCDM file into a database

SYNOPSIS

megatree-bold-loader -bold <file> -d <file> [-vhm]

OPTIONS

-b <file> or -bold <file>

Location of the TSV file from a BOLD BCDM dump, i.e. as contained in an archive such as located here as of 2023-03-06: https://bench.boldsystems.org/index.php/datapackages/Latest

-d <file> or -dbfile <file>

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.

-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-bold-loader

DESCRIPTION

This program produces a database file from a BOLD BCDM dump. Such a database provides much quicker random access to the taxonomy tree then by processing the flat file. It 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.