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#!/usr/bin/env perl
# PODNAME: change-ids-ali.pl
# ABSTRACT: Abbreviate or restore the org component of full seq ids in ALI files

use Modern::Perl '2011';
use autodie;

use Getopt::Euclid qw(:vars);
use Smart::Comments;

use Bio::MUST::Core;
use Bio::MUST::Core::Utils qw(change_suffix secure_outfile);
use aliased 'Bio::MUST::Core::Ali';
use aliased 'Bio::MUST::Core::IdMapper';


### Mapping organisms from: $ARGV_org_mapper
my $org_mapper = IdMapper->load($ARGV_org_mapper);

for my $infile (@ARGV_infiles) {

    ### Processing: $infile
    my $ali = Ali->load($infile);
    $ali->dont_guess if $ARGV_noguessing;

    # build id_mapper and change ids
    my $id_mapper;

    if ($ARGV_mode eq 'long2abbr') {
        $id_mapper = $ali->org_mapper_from_long_ids($org_mapper);
        $ali->shorten_ids($id_mapper);
    }
    else {          # 'abbr2long'
        $id_mapper = $ali->org_mapper_from_abbr_ids($org_mapper);
        $ali->restore_ids($id_mapper);
    }

    my $outfile = secure_outfile($infile, $ARGV_out_suffix);
    $ali->store($outfile);

    # optionally store the id mapper
    if ($ARGV_store_id_mapper) {
        my $idmfile = change_suffix($outfile, '.idm');
        $id_mapper->store($idmfile);
    }
}

__END__

=pod

=head1 NAME

change-ids-ali.pl - Abbreviate or restore the org component of full seq ids in ALI files

=head1 VERSION

version 0.252040

=head1 USAGE

    change-ids-ali.pl <infiles> --org-mapper=<file> --mode=<dir>
        [optional arguments]

=head1 REQUIRED ARGUMENTS