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#!/usr/bin/env perl
# PODNAME: idealize-ali.pl
# ABSTRACT: Discard (nearly) gap-only sites from 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(secure_outfile);
use aliased 'Bio::MUST::Core::Ali';


for my $infile (@ARGV_infiles) {

    ### Processing: $infile
    my $ali = Ali->load($infile);
    $ali->idealize($ARGV_max_res_drop_site);
    my $outfile = secure_outfile($infile, $ARGV_out_suffix);
    $ali->store($outfile);
}

__END__

=pod

=head1 NAME

idealize-ali.pl - Discard (nearly) gap-only sites from ALI files

=head1 VERSION

version 0.240390

=head1 USAGE

    idealize-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 --max[-res-drop-site]=<n>

Number of non-gap character states allowed in a site to be dropped [default:
0]. When specified as a fraction between 0 and 1, it is interpreted as
relative to the number of sequences in the ALI. By default, only shared gaps
are dropped.

=for Euclid: n.type:    number