File Coverage

blib/lib/NCBIx/Geo/Sample.pm

Criterion	Covered	Total	%
statement	15	50	30.0
branch	0	14	0.0
condition			n/a
subroutine	5	11	45.4
pod	0	6	0.0
total	20	81	24.6

package NCBIx::Geo::Sample;
use base qw(NCBIx::Geo::Base);

use warnings;
use strict;
use Carp;

use version; our $VERSION = qv('1.0.0');

{
        my %accn_of          :ATTR( :get           :set           :default<''>  :init_arg );
        my %data_dir_of      :ATTR( :get       :set       :default<''>  :init_arg );
        my %transcripts_of   :ATTR( :get    :set    :default<''>  :init_arg );

        sub START {
                my ($self, $ident, $arg_ref) = @_;

		if ( defined $arg_ref->{accn} ) { $self->load_transcripts(); }

                return;
        }

        sub transcript_ids {
                my ( $self, $arg_ref ) = @_;
                return join( ';', keys %{ $self->get_transcripts() } );
        }

        sub value {
                my ( $self, $arg_ref ) = @_;
		my $transcript_id      = defined $arg_ref->{transcript_id} ? $arg_ref->{transcript_id} : '';
                return $self->get_transcripts()->{$transcript_id}->{value};
        }

        sub call {
                my ( $self, $arg_ref ) = @_;
		my $transcript_id      = defined $arg_ref->{transcript_id} ? $arg_ref->{transcript_id} : '';
                return $self->get_transcripts()->{$transcript_id}->{call};
        }

        sub p_value {
                my ( $self, $arg_ref ) = @_;
		my $transcript_id      = defined $arg_ref->{transcript_id} ? $arg_ref->{transcript_id} : '';
                return $self->get_transcripts()->{$transcript_id}->{p_value};
        }

        sub load_transcripts {
                my ( $self, $arg_ref ) = @_;
		my $sample_accn        = $self->get_accn();
		my $transcripts        = {};

		# Calculate call data file_name and file_path_name
		my $file      = $sample_accn . '.html';
		my $path_name = $self->get_data_dir() . $file;

		my $text      = $self->_get_file_text({ file => $path_name });
		   $text      =~ m#(.*)#six;
		   $text      = $1;
		my @lines     = split( /\n/, $text );

		foreach my $line ( @lines ) {
			if ( $line =~ m/^#/ ) { next; }
			if ( $line =~ m/^
			if ( $line =~ m/^$/ ) { next; }

			my ( $transcript_id, $value, $call, $p_value ) = split( /\t/, $line );
			$transcripts->{ $transcript_id } = { value => $value, call => $call, p_value => $p_value };
		}

		$self->set_transcripts( $transcripts );
        }

}

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