—#!/usr/bin/env perl
# PODNAME: list2mapper.pl
# ABSTRACT: Build final id mapper from id list using the NCBI Taxonomy database
use
autodie;
use
Smart::Comments;
use
Bio::MUST::Core;
# 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