File Coverage

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

Criterion	Covered	Total	%
statement	24	34	70.5
branch	0	2	0.0
condition	0	3	0.0
subroutine	8	9	88.8
pod	1	1	100.0
total	33	49	67.3

package BioX::Map::CLIS::Cmd::Map;
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 infile => (
  is        => 'ro',
  format    => 's',
  short     => 'i',
  doc       => "path of one fastq file",
  default   => '',
);


option outfile => (
  is        => 'ro',
  format    => 's',
  short     => 'o',
  doc       => "path of outfile",
  default   => '',
);


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


option outdir => (
  is        => 'ro',
  format    => 's',
  short     => 'O',
  doc       => "path of outdir",
  default   => './',
);


option process_tool => (
  is        => 'ro',
  format    => 'i',
  short     => 'p',
  doc       => "cpu number used by mapping software",
  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',
  required  => 1,
  doc       => "path of genome file",
);


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 $pre_message = "please input parameters, genome is required, either infile or indir is required";
  my ($infile, $indir, $outfile, $outdir) = ($self->infile, $self->indir, $self->outfile, $self->outdir);
  $self->options_usage(1, $pre_message) unless ($infile or $indir);
  my ($genome, $tool, $process_tool, $process_sample) = ($self->genome, $self->tool, $self->process_tool, $self->process_sample);
  my $bm = BioX::Map->new(
    infile          => $infile,
    indir           => $indir,
    outfile         => $outfile,
    outdir          => $outdir,
    genome          => $genome,
    tool            => $tool,
    process_tool    => $process_tool,
    process_sample  => $process_sample,
  );
  $bm->map;
  my $m = time - $stamp;
  say "duration second:" . (time - $stamp) . "\nduration minute:" . (int($m/60));
}

1;

__END__