A basic command line application for modware loader

GAFLoader.pm

package GAFLoader;

# Other modules:
use namespace::autoclean; #removes all sugar
use Moose; #uses Moose
with 'Modware::Role::Command::WithBCS'; #imports attributes to get an instance of Bio::Chado::Schema object
extends qw/MooseX::App::Cmd::Command/; #makes this being recognized as runnable command


#code that gets executed when you run the comamnd
sub execute {
	my ($self) = @_;
	# A Bio::Chado::Schema object
	my $schema = $self->schema;
}

1;    # Magic true value required at end of module

__END__

=head1 NAME

B<GAFLoader2> - [Loads GAF file in the database]

GAFLoader2.pm

package GAFLoader2;

# Other modules:
use namespace::autoclean; #removes all sugar
use Moose; 
use YAML qw/LoadFile/; #exports LoadFile method from YAML module
with 'Modware::Role::Command::WithBCS'; #imports attributes to get an instance of Bio::Chado::Schema object
with 'Modware::Role::Command::WithLogger'; #gets a logger
with 'MooseX::ConfigFromFile'; #provides supports for loading options from a yaml config file
extends qw/MooseX::App::Cmd::Command/; #makes this being recognized as runnable command


#code that gets executed when you run the comamnd
sub execute {
	my ($self) = @_;
	# A Log::Log4perl object
	my $logger = $self->logger;
	$logger->info('i understand logging');

	# A Bio::Chado::Schema object
	my $schema = $self->schema;
}

# method that needed to be implemented to load the config file
# Read MooseX::ConfigFromFile for more
sub get_config_from_file {
	my ($self, $file) = @_;
	return LoadFile($file);
}


1;    # Magic true value required at end of module

__END__

=head1 NAME

B<GAFLoader2> - [Loads GAF file in the database]

GAFLoader3.pm

package GAFLoader3;

# Other modules:
use namespace::autoclean; #removes all sugar
use Moose; 
use YAML qw/LoadFile/; #exports LoadFile method from YAML module
with 'Modware::Role::Command::WithBCS'; #imports attributes to get an instance of Bio::Chado::Schema object
with 'Modware::Role::Command::WithLogger'; #gets a logger
with 'MooseX::ConfigFromFile'; #provides supports for loading options from a yaml config file
extends qw/MooseX::App::Cmd::Command/; #makes this being recognized as runnable command

## add your attributes here
## LWP object/url fetching yaada yaada here


#code that gets executed when you run the comamnd
sub execute {
	my ($self) = @_;
	# A Log::Log4perl object
	my $logger = $self->logger;
	$logger->info('i understand logging');

	# A Bio::Chado::Schema object
	my $schema = $self->schema;

	# 1.Prune all GO annotation here
	# 2.Log the output here

	# Add your GAF loading code here
	# 1. read your gene list
	# 2. Get GAF section from ebi
	# 3. Print the output (for practice)
	# 4. Extract feature_id and cvterm_id for GO and GeneId
	# 5. Insert them in feature_cvterm
}

# method that needed to be implemented to load the config file
# Read MooseX::ConfigFromFile for more
sub get_config_from_file {
	my ($self, $file) = @_;
	return LoadFile($file);
}


1;    # Magic true value required at end of module

__END__

=head1 NAME

B<GAFLoader3> - [Loads GAF file in the database]