Bio-MUST-Core
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bin/setup-taxdir.pl view on Meta::CPAN
#!/usr/bin/env perl
# PODNAME: setup-taxdir.pl
# ABSTRACT: Setup a local mirror of the NCBI Taxonomy (or GTDB) database
use Modern::Perl '2011';
use autodie;
use Getopt::Euclid qw(:vars);
use Smart::Comments;
use Bio::MUST::Core;
use aliased 'Bio::MUST::Core::Taxonomy';
unless ($ARGV_update_cache) {
my %args;
$args{gi_mapper} = 1 if $ARGV_gi_mapper;
$args{source } = $ARGV_source;
Taxonomy->setup_taxdir($ARGV_taxdir, \%args);
}
my $tax = Taxonomy->new( tax_dir => $ARGV_taxdir );
$tax->update_cache;
__END__
=pod
=head1 NAME
setup-taxdir.pl - Setup a local mirror of the NCBI Taxonomy (or GTDB) database
=head1 VERSION
version 0.240390
=head1 USAGE
setup-taxdir.pl --tax=<dir> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item --taxdir=<dir>
Path to the directory to be created.
=for Euclid: dir.type: string
=back
=head1 OPTIONAL ARGUMENTS
=over
=item --source=<str>
Source database from where to download taxonomy files (either NCBI or GTDB,
respectively designated as C<ncbi> and C<gtdb>) [default: ncbi].
=for Euclid: str.type: string, str eq 'ncbi' || str eq 'gtdb'
str.type.error: <str> must be on ncbi or gtdb (not str)
str.default: "ncbi"
=item --update-cache
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