File Coverage

blib/lib/Bio/MUST/Apps/FortyTwo/RunProcessor.pm

Criterion	Covered	Total	%
statement	36	69	52.1
branch	0	14	0.0
condition			n/a
subroutine	12	17	70.5
pod	0	1	0.0
total	48	101	47.5

package Bio::MUST::Apps::FortyTwo::RunProcessor;
# ABSTRACT: Internal class for forty-two tool
$Bio::MUST::Apps::FortyTwo::RunProcessor::VERSION = '0.213470';
use Moose;
use namespace::autoclean;

use autodie;
use feature qw(say);

use Smart::Comments;                    # logging always enabled here

use Carp;
use List::AllUtils;
use Path::Class qw(dir file);

use Parallel::Batch;

use Bio::MUST::Core;
use Bio::MUST::Drivers;
use aliased 'Bio::MUST::Apps::FortyTwo::AliProcessor';

with 'Bio::MUST::Apps::Roles::RunProcable',
     'Bio::MUST::Core::Roles::Taxable';


has 'run_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'phylogenomic',
);

has '+out_suffix' => (
    default  => '-42',
);


has 'query_orgs' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Str]',
    required => 1,
    handles  => {
        'count_query_orgs' => 'count',
          'all_query_orgs' => 'elements',
    },
);


# blast_args


has 'ref_brh' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'on',
);

has 'ref_bank_dir' => (
    is       => 'ro',
    isa      => 'Str',
);

has 'ref_org_mapper' => (
    is       => 'ro',
    isa      => 'Bio::MUST::Core::IdMapper',
    coerce   => 1,
    handles  => {
        ref_bank_for => 'abbr_id_for',
    },
);

has 'ref_orgs' => (
    traits   => ['Array'],
    is       => 'ro',
    isa      => 'ArrayRef[Str]',
    default  => sub { [] },
    handles  => {
        'count_ref_orgs' => 'count',
          'all_ref_orgs' => 'elements',
    },
);

has 'ref_org_mul' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 1.0,
);

has 'ref_score_mul' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 1.0,
);


has 'tol_check' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'off',
);

has 'tol_bank_dir' => (
    is       => 'ro',
    isa      => 'Str',
);

has 'tol_bank' => (
    is       => 'ro',
    isa      => 'Str',
);

has 'tol_blastdb' => (
    is       => 'ro',
    isa      => 'Maybe[Bio::MUST::Drivers::Blast::Database]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_tol_blastdb',
);


# trim_homologues

# trim_max_shift

# trim_extra_margin


has 'merge_orthologues' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'off',
);

has 'merge_min_ident' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 0.9,
);

has 'merge_min_len' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 40,
);


has 'aligner_mode' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'blast',
);

has 'ali_skip_self' => (
    is      => 'ro',
    isa     => 'Str',
    default => 'off',
);

has 'ali_cover_mul' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 1.1,
);

has 'ali_keep_lengthened_seqs' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'on',
);

has 'ali_keep_old_new_tags' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'off',
);


has 'tax_reports' => (
    is       => 'ro',
    isa      => 'Str',
    default  => 'on',
);

# tax_dir

has 'tax_min_hits' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 1,
);

has 'tax_max_hits' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 10000,
);

has 'tax_min_ident' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 0,
);

has 'tax_min_len' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 0,
);

has 'tax_min_score' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 0,
);

has 'tax_score_mul' => (
    is       => 'ro',
    isa      => 'Num',
    default  => 0,
);


# bank_dir

# orgs

# infiles

# debug_mode

# threads

has '_ref_blastdb_by_org' => (
    traits   => ['Hash'],
    is       => 'ro',
    isa      => 'HashRef[Bio::MUST::Drivers::Blast::Database]',
    init_arg => undef,
    lazy     => 1,
    builder  => '_build_ref_blastdb_by_org',
    handles  => {
        ref_blastdb_for => 'get',
    },
);


## no critic (ProhibitUnusedPrivateSubroutines)

sub _build_ref_blastdb_by_org {
    my $self = shift;

    # tie probably useless here but ensuring reproducible logs
    tie my %ref_blastdb_for, 'Tie::IxHash';

    for my $ref_org ($self->all_ref_orgs) {
        $ref_blastdb_for{$ref_org} = Bio::MUST::Drivers::Blast::Database->new(
            file => file(
                $self->ref_bank_dir,
                $self->ref_bank_for($ref_org)
            )
        );
    }

    return \%ref_blastdb_for;
}


sub _build_tol_blastdb {
    my $self = shift;

    return if $self->tol_check eq 'off';

    my $tolfile = file( $self->tol_bank_dir, $self->tol_bank );
    #### [RUN] TOL bank in use: $tolfile->stringify
    return Bio::MUST::Drivers::Blast::Database->new( file => $tolfile );
}

## use critic


sub BUILD {
    my $self = shift;

    unless ($self->ref_brh eq 'off') {
        croak '[RUN] Error: ref_bank_dir missing from config file; aborting!'
            unless $self->ref_bank_dir;

        croak '[RUN] Error: ref_org_mapper missing from config file; aborting!'
            unless $self->ref_org_mapper;

        croak '[RUN] Error: BLAST databases missing from ref_org_mapper;'
            . ' aborting!'
            if List::AllUtils::any {
                !defined $self->ref_bank_for($_)
            } $self->all_ref_orgs
        ;
    }

    # TODO: revise this but not sure this is really needed

#     if ($self->aligner eq 'off' && $self->run_mode eq 'phylogenomic') {
#         croak 'Error: cannot disable aligner with nucleotide banks; aborting!'
#             if List::AllUtils::any {
#                 $_->{bank_type} eq 'nucl'
#             } $self->all_orgs
#         ;
#     }
#
#     if ($self->aligner =~ m/exonerate|exoblast/xms) {
#         croak 'Error: cannot use exonerate with protein banks; aborting!'
#             if List::AllUtils::any {
#                 $_->{bank_type} eq 'prot'
#             } $self->all_orgs
#         ;
#     }

    # build optional output dir
    if ($self->out_dir) {
        my $dir = dir($self->out_dir)->relative;
        $dir->mkpath();
    }

    if ($self->threads > 1) {
        ### [RUN] Multithreading is on: $self->threads
        ### [RUN] Logging data will be mixed-up!
    }

    # spawn Taxonomy only once (especially useful for multithreading)
    $self->tax;

    # create job queue
    my $batch = Parallel::Batch->new( {
        maxprocs => $self->threads,
        jobs     => [ $self->all_infiles ],
        code     => sub {                       # closure (providing $self)
                        my $infile = shift;
                        ### [RUN] Processing ALI: $infile
                        return AliProcessor->new(
                            run_proc => $self,
                            ali      => $infile,
                        );
                    },
    } );

    # launch jobs
    $batch->run();

    return;
}


__PACKAGE__->meta->make_immutable;
1;

__END__

=pod

=head1 NAME

Bio::MUST::Apps::FortyTwo::RunProcessor - Internal class for forty-two tool

=head1 VERSION

version 0.213470

=head1 AUTHOR

Denis BAURAIN <[e-mail]>

=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