File Coverage

lib/App/SimulateReads/Command/QualityDB.pm

Criterion	Covered	Total	%
statement	6	24	25.0
branch	0	4	0.0
condition			n/a
subroutine	2	7	28.5
pod	2	3	66.6
total	10	38	26.3

package App::SimulateReads::Command::QualityDB;
# ABSTRACT: qualitydb command class. Manage quality profile database.

use App::SimulateReads::Base 'class';
use App::SimulateReads::Quality::Handle;

extends 'App::SimulateReads::CLI::Command';

our $VERSION = '0.06'; # VERSION

has 'db' => (
	is         => 'ro',
	isa        => 'App::SimulateReads::Quality::Handle',
	builder    => '_build_db',
	lazy_build => 1,
	handles    => [qw/insertdb restoredb deletedb make_report/]
);

sub _build_db {
	return App::SimulateReads::Quality::Handle->new;
}

override 'opt_spec' => sub {
	super
};

sub subcommand_map {
	add     => 'App::SimulateReads::Command::QualityDB::Add',
	remove  => 'App::SimulateReads::Command::QualityDB::Remove',
	restore => 'App::SimulateReads::Command::QualityDB::Restore'
}

sub validate_args {
	my ($self, $args) = @_;
	die "Too many arguments: '@$args'\n" if @$args;
}

sub execute {
	my ($self, $opts, $args) = @_;
	return $self->_print_report;
}

sub _print_report {
	my $self = shift;
	my $report_ref = $self->make_report;
	return if not defined $report_ref;

	my $format = "\t%*s\t%*s\t%*s\t%*s\n";
	my ($s1, $s2, $s3, $s4) = map {length} qw/sequencing_system/x4;
	printf $format => $s1, "sequencing system", $s2, "size", $s3, "source", $s4, "provider";

	for my $sequencing_system (sort keys %$report_ref) {
		my $attr = $report_ref->{$sequencing_system};
		for my $entry (sort { $a->{size} <=> $b->{size} } @$attr) {
			printf $format => $s1, $sequencing_system, $s2, $entry->{size}, $s3, $entry->{source}, $s4, $entry->{provider};
		}
	}
}

__END__

=pod

=encoding UTF-8

=head1 NAME

App::SimulateReads::Command::QualityDB - qualitydb command class. Manage quality profile database.

=head1 VERSION

version 0.06

=head1 SYNOPSIS

 simulate_reads qualitydb
 simulate_reads qualitydb [options]
 simulate_reads qualitydb <command>

 Options:
  -h, --help               brief help message
  -M, --man                full documentation

 Subcommands:
  add                      add a new quality profile to database
  remove                   remove an user quality profle from database
  restore                  restore the database

=head1 DESCRIPTION

B<simulate_reads> will read the given input file and do something
useful with the contents thereof.

=head1 AUTHOR

Thiago L. A. Miller <[e-mail]>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2017 by Teaching and Research Institute from Sírio-Libanês Hospital.

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut