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lib/Bio/ConnectDots/ConnectorSet/HG_U133_Plus_2_annot_csv.pm  view on Meta::CPAN

package Bio::ConnectDots::ConnectorSet::HG_U133_Plus_2_annot_csv;
use strict;
use vars qw(@ISA);
use Bio::ConnectDots::ConnectorSet;
@ISA = qw(Bio::ConnectDots::ConnectorSet);

sub parse_entry {
  my ($self) = @_;
  my $input_fh=$self->input_fh;
  	while (<$input_fh>) {
    		chomp;
    		if (/^"Probe Set ID"/) {
      			next;
    		}
    	
	my @field_array = split /","/;
    
    		my $probeSetID = $field_array[0];
    		$probeSetID =~ s/\"//;
		if ($probeSetID ne '---') {
		$self->put_dot('ProbeSet_ID', $probeSetID);
                }
                              
    		my $chip = $field_array[1];
		if ($chip ne '---') {
		$self->put_dot('Chip', $chip);
   		}

		my $organism = $field_array[2];
		if ($organism ne '---') {
		$self->put_dot('Organism', $organism);
		}

		my $sequenceType = $field_array[4];
		if ($sequenceType ne '---') {
                $self->put_dot('Sequence_Type', $sequenceType);
		}

		my $sequenceSource = $field_array[5];
		if ($sequenceSource ne '---') {
		$self->put_dot('Sequence_Source', $sequenceSource);
		}

		my $SDF = $field_array[6];
		if ($SDF ne '---') {
        	$SDF =~ s/\.\d+//;
		$self->put_dot('SequenceDerivedFrom', $SDF);
       		}
 
		my $geneSymbol=$field_array[12];
		if ($geneSymbol ne '---') {
		$self->put_dot('GeneSymbol', $geneSymbol);
		}	
		
		my $location=$field_array[13];
                if ($location ne '---') {
                $self->put_dot('Location', $location);
                }
	
		my $unigene = $field_array[14];
        	$unigene =~ s/\s*\/\/\s*\S*\s*\S*\s*\S*//;