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#!/usr/bin/env perl
# PODNAME: prune-ali.pl
# ABSTRACT: Prune sequences from ALI files based on id lists

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::IdList';


my $method = $ARGV_from_must ? 'load_lis' : 'load';

for my $infile (@ARGV_infiles) {

    ### Processing: $infile
    my $list = IdList->$method($infile);

    $infile =~ s/$_//xms for @ARGV_in_strip;
    my $alifile = change_suffix($infile, '.ali');
    ### Filtering sequences in: $alifile
    my $ali = Ali->load($alifile);
    $ali->dont_guess if $ARGV_noguessing;

    # optionally negate list
    $list = $list->negative_list($ali) if $ARGV_negate_list;

    # apply list to Ali
    my $pruned_ali = $ARGV_reorder ? $list->reordered_ali($ali)
                   :                 $list->filtered_ali($ali)
    ;

    my $outfile = secure_outfile($alifile, $ARGV_out_suffix);
    ### Output alignment in: $outfile
    $pruned_ali->store($outfile);
}

__END__

=pod

=head1 NAME

prune-ali.pl - Prune sequences from ALI files based on id lists

=head1 VERSION

version 0.252040

=head1 USAGE

    prune-ali.pl <infiles> [optional arguments]

=head1 REQUIRED ARGUMENTS

=over

=item <infiles>

Path to input IDL files [repeatable argument].

=for Euclid: infiles.type: readable
    repeatable

=back

=head1 OPTIONAL ARGUMENTS

=over

=item --in[-strip]=<str>

Substring(s) to strip from infile basenames before attempting to derive other
infile (e.g., ALI files) and outfile names [default: none].

=for Euclid: str.type: string
    repeatable

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

Suffix to append to (possibly stripped) infile basenames for deriving
outfile names [default: none]. When not specified, outfile names are taken
from infiles but original infiles are preserved by being appended a .bak
suffix.

=for Euclid: suffix.type: string

=item --[no]guessing

[Don't] guess whether sequences are aligned or not [default: yes].

=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 --negate-list

Interpret the list as a negative list instead of a positive list [default:
no]. This means that seqs corresponding to listed ids are discarded.

=item --reorder

Reorder sequences following list [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