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bin/app-len-ids-ali.pl  view on Meta::CPAN

#!/usr/bin/env perl
# PODNAME: app-len-ids-ali.pl
# ABSTRACT: Appends seq lengths to ids in ALI files (as SCaFoS)

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

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

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


for my $infile (@ARGV_infiles) {

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

    # append seq lengths to ids
    my $idm = $ali->len_mapper;
    $ali->restore_ids($idm);

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

__END__

=pod

=head1 NAME

app-len-ids-ali.pl - Appends seq lengths to ids in ALI files (as SCaFoS)

=head1 VERSION

version 0.240390

=head1 USAGE

    app-len-ids-ali.pl <infiles> [optional arguments]

=head1 REQUIRED ARGUMENTS

=over

=item <infiles>

Path to input ALI files [repeatable argument].

=for Euclid: infiles.type: readable
    repeatable

=back

=head1 OPTIONAL ARGUMENTS

=over

=item --out[-suffix]=<suffix>