File Coverage

blib/lib/BioX/Map/CLIS/Cmd/MapCompare.pm

Criterion	Covered	Total	%
statement	24	38	63.1
branch	0	2	0.0
condition			n/a
subroutine	8	9	88.8
pod	1	1	100.0
total	33	50	66.0

package BioX::Map::CLIS::Cmd::MapCompare;
use Modern::Perl;
use IO::All;
use Carp "confess";
use Moo;
use MooX::Options prefer_commandline => 1, with_config_from_file => 1;
use MooX::Cmd;
use BioX::Map;
use Types::Standard qw(Int Str Bool Enum);

our $VERSION = '0.0.12'; # VERSION:
# ABSTRACT: a wrapper for mapping software


around _build_config_identifier => sub { 'berry' };
around _build_config_prefix => sub { 'biox_map' };



option indir => (
  is        => 'ro',
  format    => 's',
  short     => 'i',
  default   => '',
  doc       => "path of indir include fastq files",
);


option outdir => (
  is        => 'ro',
  format    => 's',
  short     => 'o',
  doc       => "path of output dir include mapping result",
  default   => './',
);


option summary_file => (
  is        => 'ro',
  format    => 's',
  short     => 's',
  doc       => 'path of summary file',
  default   => "summary.txt",
);


option process_tool => (
  is        => 'ro',
  format    => 'i',
  short     => 'p',
  doc       => "cpu number used by soap or bwa",
  default   => 1,
);


option process_sample => (
  is        => 'ro',
  format    => 'i',
  short     => 'P',
  doc       => "number of samples running parallel",
  default   => 1,
);


option genome => (
  is        => 'ro',
  format    => 's',
  short     => 'g',
  doc       => "path of genome file",
  required  => 1,
);


option tool => (
  is        => 'ro',
  isa       => Enum['soap', 'bwa'],
  format    => 's',
  short     => 't',
  required  => 1,
  default   => 'soap',
  doc       => "mapping software",
);


sub execute {
  my ($self, $args_ref, $chain_ref) = @_;
  my $stamp = time;
  my $pre_message = "please input parameters, indir is required";
  my ($indir, $outdir) = ($self->indir, $self->outdir);
  $self->options_usage(1, $pre_message) unless ( $indir);
  my ($genome, $tool, $process_tool, $process_sample) = ($self->genome, $self->tool, $self->process_tool, $self->process_sample);
  my $bm = BioX::Map->new(
    indir           => $indir,
    outdir          => $outdir,
    genome          => $genome,
    tool            => $tool,
    process_tool    => $process_tool,
    process_sample  => $process_sample,
  );
  $bm->map;
  $bm->tool('bwa');
  $bm->map;
  my $summary = $self->summary_file;
  system("biox-map compare -i $outdir -o $summary -s soap -b bwa");
  my $m = time - $stamp;
  say "duration second" . (time - $stamp) . "\nduration minute" . (int ($m / 60));
}

1;

__END__