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lib/Bio/Tradis/CommandLine/TradisAnalysis.pm  view on Meta::CPAN

package Bio::Tradis::CommandLine::TradisAnalysis;
$Bio::Tradis::CommandLine::TradisAnalysis::VERSION = '1.4.5';
# ABSTRACT: Perform full tradis analysis


use Moose;
use Getopt::Long qw(GetOptionsFromArray);
use Cwd qw(abs_path cwd);
use Bio::Tradis::RunTradis;
use Try::Tiny;

has 'args'        => ( is => 'ro', isa => 'ArrayRef', required => 1 );
has 'script_name' => ( is => 'ro', isa => 'Str',      required => 1 );
has 'fastqfile'   => ( is => 'rw', isa => 'Str',      required => 0 );
has 'tag'         => ( is => 'rw', isa => 'Maybe[Str]',      required => 0 );
has 'mismatch' => ( is => 'rw', isa => 'Int', required => 0, default => 0 );
has 'tagdirection' =>
  ( is => 'rw', isa => 'Str', required => 0, default => '3' );
has 'reference' => ( is => 'rw', isa => 'Str',  required => 0 );
has 'help'      => ( is => 'rw', isa => 'Bool', required => 0 );
has 'mapping_score' =>
  ( is => 'rw', isa => 'Int', required => 0, default => 30 );
has 'min_seed_len' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
has 'smalt' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'smalt_k' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
has 'smalt_s' => ( is => 'rw', isa => 'Maybe[Int]', required => 0 );
has 'smalt_y' => ( is => 'rw', isa => 'Maybe[Num]', required => 0, default => 0.96 );
has 'smalt_r' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => -1 );
has 'smalt_n' => ( is => 'rw', isa => 'Maybe[Int]', required => 0, default => 1 );
has 'essentiality' => ( is => 'rw', isa => 'Bool',  required => 0, default => 0);

has 'verbose' => ( is => 'rw', isa => 'Bool', default => 0 );
has 'samtools_exec' => ( is => 'rw', isa => 'Str', default => 'samtools' );

has '_output_directory' => (
    is       => 'rw',
    isa      => 'Str',
    required => 0,
    lazy     => 1,
    builder  => '_build__output_directory'
);

has '_stats_handle' => (
    is       => 'ro',
    isa      => 'FileHandle',
    required => 0,
    lazy     => 1,
    builder  => '_build__stats_handle'
);

sub BUILD {
    my ($self) = @_;

    my (
        $fastqfile, $tag,     $td,      $mismatch, $ref,$smalt_n, $essentiality, $min_seed_len, $smalt,
        $map_score, $smalt_k, $smalt_s, $smalt_y, $smalt_r, $help, $verbose,$samtools_exec
    );

    GetOptionsFromArray(
        $self->args,
        'f|fastqfile=s'     => \$fastqfile,
        't|tag=s'           => \$tag,
        'td|tagdirection=i' => \$td,
        'mm|mismatch=i'     => \$mismatch,
        'r|reference=s'     => \$ref,
        'm|mapping_score=i' => \$map_score,
        'k|min_seed_len=i'  => \$min_seed_len,
        's|smalt'           => \$smalt,
        'sk|smalt_k=i'      => \$smalt_k,
        'ss|smalt_s=i'      => \$smalt_s,