File Coverage

blib/lib/BioX/CLPM/Sequence.pm

Criterion	Covered	Total	%
statement	3	3	100.0
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	4	4	100.0

package BioX::CLPM::Sequence;
use base qw(BioX::CLPM::Base);
use Bio::Perl qw(read_sequence);
use Class::Std;
use Class::Std::Utils;

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('0.0.1');

{
        my %sequence_of         :ATTR( :get          :set          :default<''>    :init_arg );
        my %sequence_id_of      :ATTR( :get       :set       :default<''>    :init_arg );
        my %cl_sequence_of      :ATTR( :get       :set       :default<''>    :init_arg );
        my %ann_cl_sequence_of  :ATTR( :get   :set   :default<''>    :init_arg );
        my %fragments_of        :ATTR( :get         :set         :default<[]>    :init_arg );

        sub START {
                my ( $self, $ident, $arg_ref ) = @_;
                if ( $arg_ref ) { $self->_load( $arg_ref ); }
                return;
	}

        sub fragments { my ( $self ) = @_; return @{ $self->get_fragments() }; }

        sub _load {
                my ( $self, $arg_ref ) = @_;
                #my $sequence_id = defined $arg_ref->{sequence_id} ?
                if ( defined $arg_ref->{sequence_id} ) {
                        $self->_load_from_db( $arg_ref );
                }
		elsif ( defined $arg_ref->{sequence} ) {
#                        $self->_load_from_sequence( $arg_ref );
		}
		elsif ( defined $arg_ref->{file} ) {
                        $self->_load_from_file( $arg_ref );
		}
#		if(defined $arg_ref->{linker}){
#			if( $self->get_cl_sequence eq ''){
#				$self->mark_cl_sites( { linker=>$arg_ref->{linker} } );
#			}
#		}
	}

        sub _load_from_file {
                my ( $self, $arg_ref ) = @_;
		my $file = $arg_ref->{file} ? $arg_ref->{file} : '';
		my $sequence;
		if ( -e $file ) {
			# Guess file format from extension with read_sequence()
			my $seq_object = read_sequence( $file );
			   $sequence   = $seq_object->seq();
		}
                $self->set_sequence( $sequence );
		warn "SEQUENCE _load_from_file() file $file sequence $sequence \n";
		return;
	}

        sub insert {
                my ( $self, $arg_ref ) = @_;
                my $sequence = defined $arg_ref->{sequence} ?
                                    $arg_ref->{sequence} :
                                    $self->get_sequence();
                if ( $sequence ) { $self->set_sequence($sequence); }

		# Calculate cl_sequence and ann_cl_sequence
		# TODO
		my $cl_sequence;
		my $ann_cl_sequence;

                my $sql  = 'insert into sequences (sequence, cl_sequence, ann_cl_sequence) ';
                   $sql .= "values ('$sequence', '$cl_sequence', '$ann_cl_sequence')";
                $self->sqlexec( $sql );
                   $sql  = 'select LAST_INSERT_ID()';
                my ( $sequence_id ) = $self->sqlexec( $sql, '\@@' );

                $self->set_sequence_id( $sequence_id );
                $self->set_sequence( $sequence );
                $self->set_cl_sequence( $cl_sequence );
                $self->set_ann_cl_sequence( $ann_cl_sequence );
        }

        sub _load_from_db {
                my ( $self, $arg_ref ) = @_;
                my $sequence_id = defined $arg_ref->{sequence_id} ?
                                    $arg_ref->{sequence_id} :
                                    $self->get_sequence_id();

                if ( defined $arg_ref->{sequence_id} ) {
                        $self->set_sequence_id($sequence_id);
                }

                my $sql  = 'select sequence, cl_sequence, ann_cl_sequence ';
                   $sql .= "from sequences where sequence_id = '$sequence_id'";
                my ( $sequence, $cl_sequence, $ann_cl_sequence ) = $self->sqlexec( $sql, '@' );
                $self->set_sequence( $sequence );
                $self->set_cl_sequence( $cl_sequence );
                $self->set_ann_cl_sequence( $ann_cl_sequence );
        }

#        sub _load_from_sequence{
#                my ( $self, $arg_ref ) = @_;
#                my $sequence = defined $arg_ref->{sequence} ?
#                                    $arg_ref->{sequence} :
#                                    $self->get_sequence();
#                if ( defined $arg_ref->{sequence} ) {
#                        $self->set_sequence(uc($sequence));
#                }
#                return;
#        }

#	sub mark_cl_sites{
#		my ($self, $arg_ref) = @_;
#		my $end1 = $arg_ref->{linker}->get_end1();
#		my $end2 = $arg_ref->{linker}->get_end2();
#        	foreach my $amino_acid (split('', $end1 . $end2)){
#                	$amino_acid = uc($amino_acid);
#               		my $amino_acid_lc = lc($amino_acid);
#			my $sequence = $self->get_sequence();
#                	$sequence=~s/$amino_acid/$amino_acid_lc/g;
#			$self->set_cl_sequence($sequence);
#		}
#	}
}

1; # Magic true value required at end of module
__END__