#!/usr/bin/env perl
# PODNAME: list2mapper.pl
# ABSTRACT: Build final id mapper from id list using the NCBI Taxonomy database
use Modern::Perl '2011';
use autodie;
use Getopt::Euclid qw(:vars);
use Bio::MUST::Core::Utils qw(change_suffix);
# build taxonomy object
my $tax = Taxonomy->new_from_cache( tax_dir => $ARGV_taxdir );
my $method = $ARGV_from_must ? 'load_lis' : 'load';
for my $infile (@ARGV_infiles) {
### Processing: $infile
my $list = IdList->$method($infile);
my $mapper = $tax->tax_mapper(
$list, { append_acc => $ARGV_append_acc }
);
my $outfile = change_suffix($infile, '.final-idm');
$mapper->store($outfile);
}
__END__
=pod
=head1 NAME
list2mapper.pl - Build final id mapper from id list using the NCBI Taxonomy database
=head1 VERSION
version 0.180140
=head1 USAGE
list2mapper.pl --taxdir=<dir> <infiles> [optional arguments]
=head1 REQUIRED ARGUMENTS
=over
=item <infiles>
Path to input IDL files [repeatable argument].
=for Euclid: infiles.type: readable
repeatable
=item --taxdir=<dir>
Path to local mirror of the NCBI Taxonomy database.
=for Euclid: dir.type: string
=back
=head1 OPTIONAL ARGUMENTS
=over
=item --from-must
Consider the input file as generated by ed/treeplot [default: no]. Currently,
this switches to the legacy .lis format (instead of the modern .idl format).
=item --append-acc
Append accession (or gi) number to organism name [default: no].
=item --version
=item --usage
=item --help
=item --man
Print the usual program information
=back
=head1 AUTHOR
Denis BAURAIN <denis.baurain@uliege.be>
=head1 COPYRIGHT AND LICENSE
This software is copyright (c) 2013 by University of Liege / Unit of Eukaryotic Phylogenomics / Denis BAURAIN.
This is free software; you can redistribute it and/or modify it under
the same terms as the Perl 5 programming language system itself.
=cut